Gene expression patterns under conditions of oxidative stress in Geobacter uraniumreducens
Ontology highlight
ABSTRACT:
ORGANISM(S): Geotalea uraniireducens Geotalea uraniireducens Rf4
PROVIDER: GSE12455 | GEO | 2009/06/04
SECONDARY ACCESSION(S): PRJNA113015
REPOSITORIES: GEO
Similar Datasets
Project description:Geobacteraceae transfer electrons from a donor such as acetate to an electron acceptor such as Fe(III) or U(VI). Geobacter uraniireducens is found in uranium-contaminated sites and plays an important role in in situ bioremediation. In this experiment, gene expression was compared between G. uraniireducens cultures grown in sediments from a uranium contaminated site amended with acetate and cultures grown in acetate/fumarate medium. Keywords: two-condition comparison
2008-10-20 | GSE10920 | GEO
Project description:Mahadevan2006 - Genome-scale metabolic
network of Geobacter sulfurreducens (iRM588)
This model is described in the article:
Characterization of
metabolism in the Fe(III)-reducing organism Geobacter
sulfurreducens by constraint-based modeling.
Mahadevan R, Bond DR, Butler JE,
Esteve-Nuñez A, Coppi MV, Palsson BO, Schilling CH, Lovley
DR.
Appl. Environ. Microbiol. 2006 Feb;
72(2): 1558-1568
Abstract:
Geobacter sulfurreducens is a well-studied representative of
the Geobacteraceae, which play a critical role in organic
matter oxidation coupled to Fe(III) reduction, bioremediation
of groundwater contaminated with organics or metals, and
electricity production from waste organic matter. In order to
investigate G. sulfurreducens central metabolism and electron
transport, a metabolic model which integrated genome-based
predictions with available genetic and physiological data was
developed via the constraint-based modeling approach.
Evaluation of the rates of proton production and consumption in
the extracellular and cytoplasmic compartments revealed that
energy conservation with extracellular electron acceptors, such
as Fe(III), was limited relative to that associated with
intracellular acceptors. This limitation was attributed to lack
of cytoplasmic proton consumption during reduction of
extracellular electron acceptors. Model-based analysis of the
metabolic cost of producing an extracellular electron shuttle
to promote electron transfer to insoluble Fe(III) oxides
demonstrated why Geobacter species, which do not produce
shuttles, have an energetic advantage over shuttle-producing
Fe(III) reducers in subsurface environments. In silico analysis
also revealed that the metabolic network of G. sulfurreducens
could synthesize amino acids more efficiently than that of
Escherichia coli due to the presence of a pyruvate-ferredoxin
oxidoreductase, which catalyzes synthesis of pyruvate from
acetate and carbon dioxide in a single step. In silico
phenotypic analysis of deletion mutants demonstrated the
capability of the model to explore the flexibility of G.
sulfurreducens central metabolism and correctly predict mutant
phenotypes. These results demonstrate that iterative modeling
coupled with experimentation can accelerate the understanding
of the physiology of poorly studied but environmentally
relevant organisms and may help optimize their practical
applications.
This model is hosted on
BioModels Database
and identified by:
MODEL1507180000.
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 | MODEL1507180000 | BioModels
Project description:G. uraniireducens was isolated from a subsurface site in Rifle, CO undergoing in situ uranium bioremediation. Sediments from the Rifle site were heat-sterilized, amended with acetate to simulate in situ bioremediation conditions, and inoculated with G. uraniireducens. Gene transcript abundance in these cells using sediment Fe(III) and Mn(IV) oxides as the electron acceptor were compared with transcript levels in cells grown with fumarate as the electron acceptor. Additional comparisons were made between cells grown on synthetic Fe(III) or Mn(IV) oxides and cells grown on fumarate. 3 biological replicates hybridized in duplicate
2010-07-21 | E-GEOD-12874 | biostudies-arrayexpress
Project description:G. uraniireducens was isolated from a subsurface site in Rifle, CO undergoing in situ uranium bioremediation. Sediments from the Rifle site were heat-sterilized, amended with acetate to simulate in situ bioremediation conditions, and inoculated with G. uraniireducens. Gene transcript abundance in these cells using sediment Fe(III) and Mn(IV) oxides as the electron acceptor were compared with transcript levels in cells grown with fumarate as the electron acceptor. Additional comparisons were made between cells grown on synthetic Fe(III) or Mn(IV) oxides and cells grown on fumarate.
2010-07-22 | GSE12874 | GEO
Project description:The Geobacter species evolved respiratory versatility to utilize a wide range of terminal electron acceptors. To explore this adaptive mechanism, Fe(III) citrate, hydrous ferric oxide, and fumarate were selected as electron acceptors, and the methylome and metabolome of Geobacter sulfurreducens PCA grown on each electron acceptor were investigated via third-generation, single-molecule real-time DNA sequencing.Results showed that the patterns of 4-methylcytosine (m4C) and 6-methyladenine (m6A) modification were all varied in different electron acceptor cultures. Moreover, genes (e.g., GSU0466 and GSU1467) with low expression levels generally had high methylation levels. These findings suggest that m4C and m6A modifications play a role in the adaption of G. sulfurreducens to diverse electron acceptors, and DNA methylation may be involved in the adaption mainly via gene expression regulation.
2021-08-31 | GSE157224 | GEO
Project description:This SuperSeries is composed of the following subset Series: GSE21312: Gene expression in a Geobacter sulfurreducens strain adapted for faster Fe(III) oxide reduction grown with ferric citrate as an electron acceptor GSE21313: Gene expression in a Geobacter sulfurreducens strain adapted for faster Fe(III) oxide reduction grown with fumarate as an electron acceptor Refer to individual Series
2011-04-11 | E-GEOD-21322 | 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: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:Transcriptomic analysis of interspecies electron transfer between Geobacter metallireducens and Geobacter sulfurreducens with the addition of three materials
| PRJNA383096 | ENA