Aromatics Degradation in Geobacter metallireducens
Ontology highlight
ABSTRACT:
ORGANISM(S): Geobacter metallireducens GS-15
PROVIDER: GSE5401 | GEO | 2007/07/03
SECONDARY ACCESSION(S): PRJNA96299
REPOSITORIES: GEO
Similar Datasets
Project description:Aromatics Degradation in Geobacter metallireducens
| PRJNA96299 | ENA
Project description:Insight into the mechanisms for the anaerobic metabolism of aromatic compounds by the hyperthermophilic archaeon Ferroglobus placidus is expected to improve understanding of the degradation of aromatics in hot (> 80 °C) environments and to identify enzymes that might have biotechnological applications. Analysis of the F. placidus genome revealed genes predicted to encode enzymes homologous to those previously identified as playing a role in benzoate and phenol metabolism in mesophilic bacteria. Surprisingly, F. placidus lacks genes for an ATP-independent class II benzoyl-CoA reductase found in all strictly anaerobic bacteria, but instead has two sets of genes for ATP-consuming class I benzoyl-CoA reductases, similar to those found in facultative bacteria. The lower portion of the benzoate degradation pathway appears to be more similar to that found in the phototroph Rhodopseudomonas palustris, than the pathway reported for all heterotrophic anaerobic benzoate degraders. Many of the genes predicted to be involved in benzoate metabolism were found in one of two gene clusters. Genes for a phenol carboxylation proceeding through a phenylphosphate intermediate and for conversion of p-hydroxybenzoate to benzoyl-CoA were identified in a single gene cluster. Analysis of transcript abundance with a whole-genome microarray and quantitative PCR demonstrated that most of the genes predicted to be involved in benzoate or phenol metabolism had higher transcript abundance during growth on those substrates versus growth on acetate. These results suggest that the general strategies for benzoate and phenol metabolism may be highly conserved between microorganisms living in moderate and hot environments, and that anaerobic metabolism of aromatic compounds might be analyzed in a wide range of environments with similar molecular targets. A four chip study using total RNA recovered from two separate cultures of Ferroglobus placidus DSM 10642 grown with 1 mM sodium benzoate (experimental condition) and two separate cultures of Ferroglobus placidus DSM 10642 grown on 10 mM acetate (control condition). Each chip measures the expression level of 2613 genes from Ferroglobus placidus DSM 10642 with nine 45-60-mer probe pairs (PM/MM) per gene, with three-fold technical redundancy.
2011-01-05 | E-GEOD-26421 | biostudies-arrayexpress
Project description:Insight into the mechanisms for the anaerobic metabolism of aromatic compounds by the hyperthermophilic archaeon Ferroglobus placidus is expected to improve understanding of the degradation of aromatics in hot (> 80 °C) environments and to identify enzymes that might have biotechnological applications. Analysis of the F. placidus genome revealed genes predicted to encode enzymes homologous to those previously identified as playing a role in benzoate and phenol metabolism in mesophilic bacteria. Surprisingly, F. placidus lacks genes for an ATP-independent class II benzoyl-CoA reductase found in all strictly anaerobic bacteria, but instead has two sets of genes for ATP-consuming class I benzoyl-CoA reductases, similar to those found in facultative bacteria. The lower portion of the benzoate degradation pathway appears to be more similar to that found in the phototroph Rhodopseudomonas palustris, than the pathway reported for all heterotrophic anaerobic benzoate degraders. Many of the genes predicted to be involved in benzoate metabolism were found in one of two gene clusters. Genes for a phenol carboxylation proceeding through a phenylphosphate intermediate and for conversion of p-hydroxybenzoate to benzoyl-CoA were identified in a single gene cluster. Analysis of transcript abundance with a whole-genome microarray and quantitative PCR demonstrated that most of the genes predicted to be involved in benzoate or phenol metabolism had higher transcript abundance during growth on those substrates versus growth on acetate. These results suggest that the general strategies for benzoate and phenol metabolism may be highly conserved between microorganisms living in moderate and hot environments, and that anaerobic metabolism of aromatic compounds might be analyzed in a wide range of environments with similar molecular targets.
2011-01-05 | GSE26421 | GEO
Project description:Anaerobic activation of benzene is expected to represent a novel biochemistry of environmental significance but research into the mechanisms has been stymied by a lack of a genetically tractable pure culture which unequivocally does not use molecular oxygen to activate benzene. Geobacter metallireducens grew in a medium in which benzene was the sole electron donor and Fe(III) was the sole electron acceptor with a stoichiometry of benzene loss and Fe(III) reduction consistent with benzene oxidation to carbon dioxide coupled with Fe(III) reduction. Phenol labeled with 18O was produced when the medium was labeled with H218O, as expected for a true anaerobic conversion of benzene to phenol. Gene expression patterns indicated that benzene was metabolized through a phenol intermediate rather than benzoate or toluene. Deletion of ppcB, which encodes a subunit of the phenylphosphate carboxylase, an enzyme required for phenol metabolism, inhibited metabolism of benzene. Deleting genes specific for benzoate or toluene metabolism did not. Comparison of gene expression patterns in cells grown on benzene versus cells grown on phenol revealed genes specifically expressed in benzene-grown cells. Deletion of one of these, Gmet_3376, inhibited anaerobic benzene oxidation, but not the metabolism of phenol, benzoate, or toluene. The availability of a genetically tractable pure culture that can anaerobically convert benzene to phenol with oxygen derived from water should significantly accelerate elucidation of the mechanisms by which benzene can be activated in the absence of molecular oxygen. Total RNA from three separate cultures of G. metallireducens grown with 250 µM benzene three separate cultures of G. metallireducens grown with 500 µM phenol three separate cultures of G. metallireducens grown with 1 mM benzoate three separate cultures of G. metallireducens grown with 500 µM toluene three separate cultures of G. metallireducens grown with 10 mM acetate were used to study [1] Anaerobic oxidation of benzene by G. metallireducens (Benzene vs. acetate, Benzene vs. benzoate, Benzene vs. phenol, Benzene vs. toluene) [2] Anaerobic oxidation of benzoate by G. metallireducens (Benzoate vs. acetate) [3] Anaerobic oxidation of phenol by G. metallireducens (Phenol vs. acetate) [4] Anaerobic oxidation of toluene by G. metallireducens (Toluene vs. acetate) Each chip measures the expression level of 3,627 genes from G. metallireducens DSM 7210 with nine 45-60-mer probe pairs (PM/MM) per gene, with three-fold technical redundancy.
2013-04-30 | E-GEOD-33794 | biostudies-arrayexpress
Project description:Sun2009 - Genome-scale metabolic network of
Geobacter metallireducens (iJS747)
This model is described in the article:
Genome-scale
constraint-based modeling of Geobacter metallireducens.
Sun J, Sayyar B, Butler JE, Pharkya
P, Fahland TR, Famili I, Schilling CH, Lovley DR, Mahadevan
R.
BMC Syst Biol 2009; 3: 15
Abstract:
BACKGROUND: Geobacter metallireducens was the first organism
that can be grown in pure culture to completely oxidize organic
compounds with Fe(III) oxide serving as electron acceptor.
Geobacter species, including G. sulfurreducens and G.
metallireducens, are used for bioremediation and electricity
generation from waste organic matter and renewable biomass. The
constraint-based modeling approach enables the development of
genome-scale in silico models that can predict the behavior of
complex biological systems and their responses to the
environments. Such a modeling approach was applied to provide
physiological and ecological insights on the metabolism of G.
metallireducens. RESULTS: The genome-scale metabolic model of
G. metallireducens was constructed to include 747 genes and 697
reactions. Compared to the G. sulfurreducens model, the G.
metallireducens metabolic model contains 118 unique reactions
that reflect many of G. metallireducens' specific metabolic
capabilities. Detailed examination of the G. metallireducens
model suggests that its central metabolism contains several
energy-inefficient reactions that are not present in the G.
sulfurreducens model. Experimental biomass yield of G.
metallireducens growing on pyruvate was lower than the
predicted optimal biomass yield. Microarray data of G.
metallireducens growing with benzoate and acetate indicated
that genes encoding these energy-inefficient reactions were
up-regulated by benzoate. These results suggested that the
energy-inefficient reactions were likely turned off during G.
metallireducens growth with acetate for optimal biomass yield,
but were up-regulated during growth with complex electron
donors such as benzoate for rapid energy generation.
Furthermore, several computational modeling approaches were
applied to accelerate G. metallireducens research. For example,
growth of G. metallireducens with different electron donors and
electron acceptors were studied using the genome-scale
metabolic model, which provided a fast and cost-effective way
to understand the metabolism of G. metallireducens. CONCLUSION:
We have developed a genome-scale metabolic model for G.
metallireducens that features both metabolic similarities and
differences to the published model for its close relative, G.
sulfurreducens. Together these metabolic models provide an
important resource for improving strategies on bioremediation
and bioenergy generation.
This model is hosted on
BioModels Database
and identified by:
MODEL1507180002.
To cite BioModels Database, please use:
BioModels Database:
An enhanced, curated and annotated resource for published
quantitative kinetic models.
To the extent possible under law, all copyright and related or
neighbouring rights to this encoded model have been dedicated to
the public domain worldwide. Please refer to
CC0
Public Domain Dedication for more information.
2015-07-30 | MODEL1507180002 | BioModels
Project description:Degradation of polycyclic aromatic hydrocarbons (PAHs) such as naphthalene by anaerobic microorganisms is poorly understood. Strain NaphS2, an anaerobic sulfate reducing marine delta-proteobacterium is capable of using naphthalene and the aromatic compound benzoate, as well as pyruvate, as an electron donors in the presence of sulfate. In order to identify genes involved in the naphthalene degradation pathway, we compared gene expression in NaphS2 during growth on benzoate vs. pyruvate, naphthalene vs. pyruvate, and naphthalene vs benzoate.
2010-07-22 | GSE12323 | GEO
Project description:Bioavailability of electron acceptors is probably the most limiting factor in the restoration of anoxic, contaminated environments. The oxidation of contaminants such as aromatic hydrocarbons, particularly in aquifers, often depends on the reduction of ferric iron or sulphate. We have previously detected a highly active fringe zone beneath a toluene plume at a tar-oil contaminated aquifer in Germany, where a specialized community of contaminant degraders co-dominated by Desulfobulbaceae and Geobacteraceae had established. Although on-site geochemistry links degradation to sulphidogenic processes, dominating catabolic (benzylsuccinate synthase alpha-subunit, bssA) genes detected in situ appeared more related to those of Geobacter spp. Therefore, a stable isotope probing (SIP) incubation of sediment samples with 13C7-toluene and comparative electron acceptor amendment was performed. We introduce pyrosequencing of templates from SIP microcosms as a powerful new strategy in SIP gradient interpretation (Pyro-SIP). Our results reveal the central role of Desulfobulbaceae for sulphidogenic toluene degradation in situ, and affiliate the detected bssA genes to this lineage. This, and the absence of 13C-labelled DNA of Geobacter spp. in SIP gradients preclude their relevance as toluene degraders in situ. In contrast, Betaproteobacteria related to Georgfuchsia spp. became labelled under iron-reducing conditions. Furthermore, secondary toluene degraders belonging to the Peptococcaceae detected in both treatments suggest the possibility of functional redundancy amongst anaerobic toluene degraders on site. 2 samples examined from the different electron-acceptors (sulphate or ferric iron) incubates at the time point of maximal toluene degradation.
2011-03-18 | E-GEOD-25449 | biostudies-arrayexpress
Project description:Convergent microbial biocatalysis has emerged as a promising approach for the conversion of lignin side-streams into value-added chemicals in recent decades. However, the current knowledge of metabolic pathways directing the bioconversion of lignin-related aromatics is still limited to a few microbial species and unavailable for some of these compounds. Thus, the aim of this study was to identify the genes involved in the bioconversion of aromatic compounds in Xanthomonas citri subsp. citri 306 (X. citri 306), a bacterium belonging to a compelling yet untapped genus for studies on lignin-related aromatics metabolism. For this purpose, we used an integrative approach including genome data mining, RNA-seq, enzymology and gene knockout studies. The RNA-seq analysis revealed a total of 278 to 1464 differentially expressed genes (DEGs) in the aromatic-containing conditions compared to the control XVM2m-glucose, evidencing the importance of these compounds in modulating various physiological processes of X. citri 306 beyond the pathways related to their metabolism. Moreover, this work revealed the operon molRKAB, which plays a role in the first catabolic steps of the three main monolignols (p-coumaryl, coniferyl and sinapyl alcohols), besides showing all the enzymatic steps funneling them up to the tricarboxylic acid cycle. Additionally, the study uncovered aryl aldehyde reductases and efflux strategies that likely function to protect the pathogen from aromatics toxicity. Together, these findings enhance the current understanding of Xanthomonas metabolism and transcriptional responses to lignin-related aromatic compounds, shedding light on the diverse metabolic pathways available to enable the engineering of microbial chassis dedicated to lignin valorization.
2024-08-19 | GSE252662 | GEO
Project description:Degradation of polycyclic aromatic hydrocarbons (PAHs) such as naphthalene by anaerobic microorganisms is poorly understood. Strain NaphS2, an anaerobic sulfate reducing marine delta-proteobacterium is capable of using naphthalene and the aromatic compound benzoate, as well as pyruvate, as an electron donors in the presence of sulfate. In order to identify genes involved in the naphthalene degradation pathway, we compared gene expression in NaphS2 during growth on benzoate vs. pyruvate, naphthalene vs. pyruvate, and naphthalene vs benzoate. For each experimental set, aRNA from NaphS2 was labelled Cy5 (experiment) or Cy3(control) with three biological replicates hybridized in duplicate. In addition, because of the size of the predicted genome of NaphS2, ORFs were divided into two separate array designs, designated set1 and set2, such that set1 and set2 represent two separate array designs (probe sets) to be treated separately in statistical analysis.
2010-07-21 | E-GEOD-12323 | biostudies-arrayexpress
Project description:Bioavailability of electron acceptors is probably the most limiting factor in the restoration of anoxic, contaminated environments. The oxidation of contaminants such as aromatic hydrocarbons, particularly in aquifers, often depends on the reduction of ferric iron or sulphate. We have previously detected a highly active fringe zone beneath a toluene plume at a tar-oil contaminated aquifer in Germany, where a specialized community of contaminant degraders co-dominated by Desulfobulbaceae and Geobacteraceae had established. Although on-site geochemistry links degradation to sulphidogenic processes, dominating catabolic (benzylsuccinate synthase alpha-subunit, bssA) genes detected in situ appeared more related to those of Geobacter spp. Therefore, a stable isotope probing (SIP) incubation of sediment samples with 13C7-toluene and comparative electron acceptor amendment was performed. We introduce pyrosequencing of templates from SIP microcosms as a powerful new strategy in SIP gradient interpretation (Pyro-SIP). Our results reveal the central role of Desulfobulbaceae for sulphidogenic toluene degradation in situ, and affiliate the detected bssA genes to this lineage. This, and the absence of 13C-labelled DNA of Geobacter spp. in SIP gradients preclude their relevance as toluene degraders in situ. In contrast, Betaproteobacteria related to Georgfuchsia spp. became labelled under iron-reducing conditions. Furthermore, secondary toluene degraders belonging to the Peptococcaceae detected in both treatments suggest the possibility of functional redundancy amongst anaerobic toluene degraders on site.
2011-03-18 | GSE25449 | GEO