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ABSTRACT:
PROVIDER: PRJNA828193 | ENA |
REPOSITORIES: ENA
Dataset's files
| Action | DRS | |||
|---|---|---|---|---|
| SRR18825230.fastq.gz | Fastqsanger.gz | |||
| SRR18825230_1.fastq.gz | Fastqsanger.gz | |||
| SRR18825230_2.fastq.gz | Fastqsanger.gz |
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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.
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2015-07-30 | MODEL1507180002 | BioModels
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:The ability of Geobacter species to readily donate electrons to extracellular electron acceptors makes the study of their physiology not only important for the understanding of environmental processes, but also for industrial applications such as bioelectronics and electrosynthesis. Studies in G. sulfurreducens have shown that outer surface components, such as c-type cytochromes and conductive type IV pili play an important role in direct electron transfer to extracellular electron acceptors such as Fe(III) oxides and electrodes. However, many of these thoroughly studied outer surface components, including c-type cytochromes, are not well conserved among Geobacter species. In order to better understand which components are involved in extracellular electron transfer in Geobacter species other than G. sulfurreducens, studies were conducted with its close relative G. metallireducens. Whole-genome microarray analysis revealed that 23 of the 91 putative c-type cytochromes encoded in the G. metallireducens genome were upregulated at least 2-fold in cells grown with Fe(III) oxide compared to cells in which Fe(III) citrate was provided as the terminal electron acceptor. Protein identification with liquid-chromatography/mass spectrometry detected 6 c-type cytochromes that were more abundant in the outer surface cell fraction of cells that were grown with Fe(III) oxide as the terminal electron acceptor compared to cells grown on Fe(III) citrate. 22 genes encoding c-type cytochromes were chosen for gene deletion. Deletion of 6 genes encoding for c-type cytochromes, a gene encoding for a lipopolysaccharide biosynthesis-associated protein, and a gene encoding for a NHL- repeat containing protein inhibited growth when Fe(III) oxide was provided as the electron acceptor. This study suggests that there are different roads for extracellular electron transfer in Geobacteraceae since homologous c-type cytochromes have different functions from one species to the other, and novel components not previously found to be essential for extracellular electron transfer were identified. An eight-chip study using total RNA recovered from four separate cultures of Geobacter metallireducens GS-15 grown with acetate (10mM)-Fe(III) oxide (100 mmol l-1) (experimental condition) or with acetate (10 mM)-Fe(III) citrate (55mM) (control condition) during exponential growth. Each chip measures the expression level of 3,627 genes from Geobacter metallireducens GS-15 with nine 45-60-mer probe pairs (PM/MM) per gene, with three-fold technical redundancy.
2013-02-18 | E-GEOD-40316 | biostudies-arrayexpress
Project description:Aromatics Degradation in Geobacter metallireducens
| PRJNA96299 | ENA
Project description:Geobacter species are of great interest for environmental and biotechnology applications as they can carry out direct electron transfer to insoluble metals or other microorganisms and have the ability to assimilate inorganic carbon. Here, we report on the capability and key enabling metabolic machinery of Geobacter metallireducens GS-15 to carry out CO2 fixation and direct electron transfer to iron. An updated metabolic reconstruction was generated, growth screens on targeted conditions of interest were performed, and constraint-based analysis was utilized to characterize and evaluate critical pathways and reactions in G. metallireducens. The novel capability of G. metallireducens to grow autotrophically with formate and Fe(III) was predicted and subsequently validated in vivo. Additionally, the energetic cost of transferring electrons to an external electron acceptor was determined through analysis of growth experiments carried out using three different electron acceptors (Fe(III), nitrate, and fumarate) by systematically isolating and examining different parts of the electron transport chain. The updated reconstruction will serve as a knowledgebase for understanding and engineering Geobacter and similar species.
2023-11-27 | MODEL2204190002 | BioModels