Dataset Information

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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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]

PMID: 17578578

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Project description:BACKGROUND: 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. RESULTS: The complete G. metallireducens genome contained a 300 kb island predicted to encode enzymes for the degradation of phenol, p-cresol, 4-hydroxybenzaldehyde, 4-hydroxybenzoate, benzyl alcohol, benzaldehyde, and benzoate. Toluene degradation genes were encoded in a separate region. None of these genes was found in closely related species that cannot degrade aromatic compounds. Abundant transposons and phage-like genes in the island suggest mobility, but nucleotide composition and lack of synteny with other species do not suggest a recent transfer. The inferred degradation pathways are similar to those in species that anaerobically oxidize aromatic compounds with nitrate as an electron acceptor. In these pathways the aromatic compounds are converted to benzoyl-CoA and then to 3-hydroxypimelyl-CoA. However, in G. metallireducens there were no genes for the energetically-expensive dearomatizing enzyme. Whole-genome changes in transcript levels were identified in cells oxidizing benzoate. These supported the predicted pathway, identified induced fatty-acid oxidation genes, and identified an apparent shift in the TCA cycle to a putative ATP-yielding succinyl-CoA synthase. Paralogs to several genes in the pathway were also induced, as were several putative molybdo-proteins. Comparison of the aromatics degradation pathway genes to the genome of an isolate from a contaminated field site showed very similar content, and suggested this strain degrades many of the same compounds. This strain also lacked a classical dearomatizing enzyme, but contained two copies of an eight-gene cluster encoding redox proteins that was 30-fold induced during benzoate oxidation. CONCLUSION: G. metallireducens appears to convert aromatic compounds to benzoyl-CoA, then to acetyl-CoA via fatty acid oxidation, and then to carbon dioxide via the TCA cycle. The enzyme responsible for dearomatizing the aromatic ring may be novel, and energetic investments at this step may be offset by a change in succinate metabolism. Analysis of a field isolate suggests that the pathways inferred for G. metallireducens may be applicable to modeling in situ bioremediation.

Project description:Anaerobic biodegradation of aromatic compounds under sulfate-reducing conditions is important to marine sediments. Sulfate respiration by a single bacterial strain and syntrophic metabolism by a syntrophic bacterial consortium are primary strategies for sulfate-dependent biodegradation of aromatic compounds. The objective of this study was to investigate the potential of conductive iron oxides to facilitate the degradation of aromatic compounds under sulfate-reducing conditions in marine sediments, using benzoate as a model aromatic compound. Here, in anaerobic incubations of sediments from the Pearl River Estuary, the addition of hematite or magnetite (20 mM as Fe atom) enhanced the rates of sulfate-dependent benzoate degradation by 81.8 and 91.5%, respectively, compared with control incubations without iron oxides. Further experiments demonstrated that the rate of sulfate-dependent benzoate degradation accelerated with increased magnetite concentration (5, 10, and 20 mM). The detection of acetate as an intermediate product implied syntrophic benzoate degradation pathway, which was also supported by the abundance of putative acetate- or/and H2-utilizing sulfate reducers from microbial community analysis. Microbial reduction of iron oxides under sulfate-reducing conditions only accounted for 2-11% of electrons produced by benzoate oxidation, thus the stimulatory effect of conductive iron oxides on sulfate-dependent benzoate degradation was not mainly due to an increased pool of terminal electron acceptors. The enhanced rates of syntrophic benzoate degradation by the presence of conductive iron oxides probably resulted from the establishment of a direct interspecies electron transfer (DIET) between syntrophic partners. In the presence of magnetite, Bacteroidetes and Desulfobulbaceae with potential function of extracellular electron transfer might be involved in syntrophic benzoate degradation. Results from this study will contribute to the development of new strategies for in situ bioremediation of anaerobic sediments contaminated with aromatic compounds, and provide a new perspective for the natural attenuation of aromatic compounds in iron-rich marine sediments.