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Metabolomics,Unknown,Transcriptomics,Genomics,Proteomics

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Transcription profiling of RelA mutant and wild type Geobacter sulfurreducens

ABSTRACT: This experiment tests the gene expression of the RelA mutant (ORF03691/GSU2236) versus wild type G. sulfurreducens during stationary phase growth. Batch culture, Acetate electron donor, Fumarate electron acceptor.

ORGANISM(S): Geobacter sulfurreducens

SUBMITTER: Barbara Methe

PROVIDER: E-TIGR-5000 | biostudies-arrayexpress |

REPOSITORIES: biostudies-arrayexpress

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Role of RelGsu in stress response and Fe(III) reduction in Geobacter sulfurreducens.

DiDonato Laurie N LN Sullivan Sara A SA Methé Barbara A BA Nevin Kelly P KP England Reg R Lovley Derek R DR

Journal of bacteriology 20061013 24

Geobacter species are key members of the microbial community in many subsurface environments in which dissimilatory metal reduction is an important process. The genome of Geobacter sulfurreducens contains a gene designated rel(Gsu), which encodes a RelA homolog predicted to catalyze both the synthesis and the degradation of guanosine 3',5'-bispyrophosphate (ppGpp), a regulatory molecule that signals slow growth in response to nutrient limitation in bacteria. To evaluate the physiological role of ...[more]

PMID: 17041036

Similar Datasets

Transcription profiling of wild type G. sulfurreducens DL1 strain and mutant RelA (relGsu::kan) using fumarate as an electron acceptor

Project description:This experiment tests the gene expression of the RelA mutant (ORF03691/GSU2236) versus wild type G. sulfurreducens during log phase growth. Chemostat culture, Acetate-limiting electron donor, Fumarate electron acceptor.

2007-02-15 | E-TIGR-200 | biostudies-arrayexpress

Transcription profiling of wild type G. sulfurreducens DL1 strain and mutant DLCN16 (delta-rpoS::Km) using fumarate as an electron acceptor

Project description:Wild type G. sulfurreducens DL1 strain (see Caccavo, F., Jr., D. J. Lonergan, D. R. Lovley, M. Davis, J. F. Stolz, and M. J. McInerney. 1994. Geobacter sulfurreducens sp. nov., a hydrogen- and acetate-oxidizing dissimilatory metal-reducing microorganism. Appl Environ Microbiol 60:3752-9. see also Coppi, M. V., C. Leang, S. J. Sandler, and D. R. Lovley. 2001. Development of a genetic system for Geobacter sulfurreducens. Appl Environ Microbiol 67:3180-7.) and DLCN16 mutant (.rpoS::Km) (see Nuñez, C., L. Adams, S. Childers, and D. R. Lovley. 2004. The RpoS sigma factor in the dissimilatory Fe(III)-reducing bacterium Geobacter sulfurreducens. J Bacteriol 186:5543-6.) were grown under anaerobic conditions at 30 °C in continuous culture with a 200 ml working volume as previously described (see Esteve-Nunez, A., M. Rothermich, M. Sharma, and D. Lovley. 2005. Growth of Geobacter sulfurreducens under nutrient-limiting conditions in continuous culture. Environ Microbiol 7:641-8.). Cells were cultured at a growth rate of 0.05 h-1, steady-state cell growth was obtained after 5 volume refills and was confirmed by a constant cell density and concentrations of fumarate and succinate. Acetate (5.5 mM) was the electron donor and the limiting substrate. The electron acceptor was fumarate (30mM). Three biological replicates of control and treatment cells were obtained to produce hybridizations for this experiment.

2005-01-01 | E-TIGR-128 | biostudies-arrayexpress

Gene expression patterns in a Geobacter sulfurreducens strain adapted for faster Fe(III) oxide reduction

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

Geobacter sulfurreducens

Project description:G. sulfurreducens growth with acetate as limiting electron donor versus fumarate as limiting electron acceptor

| PRJNA103799 | ENA

Methylomes of Geobacter sulfurreducens Grown on Different Terminal Electron Acceptors

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

Transcription profiling of wild type G. sulfurreducens DL1 strain and mutant DLCN16 (delta-rpoS::Km) using ferric citrate as an electron acceptor

Project description:Wild type G. sulfurreducens DL1 strain (see Caccavo, F., Jr., D. J. Lonergan, D. R. Lovley, M. Davis, J. F. Stolz, and M. J. McInerney. 1994. Geobacter sulfurreducens sp. nov., a hydrogen- and acetate-oxidizing dissimilatory metal-reducing microorganism. Appl Environ Microbiol 60:3752-9. see also Coppi, M. V., C. Leang, S. J. Sandler, and D. R. Lovley. 2001. Development of a genetic system for Geobacter sulfurreducens. Appl Environ Microbiol 67:3180-7.) and DLCN16 mutant (.rpoS::Km) (see Nuñez, C., L. Adams, S. Childers, and D. R. Lovley. 2004. The RpoS sigma factor in the dissimilatory Fe(III)-reducing bacterium Geobacter sulfurreducens. J Bacteriol 186:5543-6.) were grown under anaerobic conditions at 30 °C in continuous culture with a 200 ml working volume as previously described (see Esteve-Nunez, A., M. Rothermich, M. Sharma, and D. Lovley. 2005. Growth of Geobacter sulfurreducens under nutrient-limiting conditions in continuous culture. Environ Microbiol 7:641-8.). Cells were cultured at a growth rate of 0.05 h-1, steady-state cell growth was obtained after 5 volume refills and was confirmed by a constant cell density and concentrations of Fe(II). Acetate (5.5 mM) was the electron donor and the limiting substrate. The electron acceptor was Fe(III)-citrate (60mM). Two biological replicates of control and treatment cells were obtained to produce hybridizations for this experiment.

2005-01-01 | E-TIGR-123 | biostudies-arrayexpress

Gene expression in a Geobacter sulfurreducens strain adapted for faster Fe(III) oxide reduction grown with fumarate as an electron acceptor

Project description:Geobacter sulfurreducens PCA was put under selective pressure for rapid Fe(III) oxide reduction. The resultant strain, V1, contained five confirmed mutations and reduced Fe(III) oxide 17 times faster. One of these five mutations inactivates dcuB, a fumarate/succinate antiporter necessary for growth with fumarate as an electron acceptor. V1 dcuB+ is a V1 strain containing a wild type copy of dcuB. Whole genome DNA microarray analysis was performed in order to determine which genes are up- or down-regulated in V1 dcuB+ compared to PCA, both grown with fumarate as an electron acceptor.

2011-04-12 | GSE21313 | GEO

Transcription profiling of G sulfurreducens GGS nitrogen fixation

Project description:G. sulfurreducens (ATCC #51573) was obtained from the laboratory culture collection of Dr. Derek Lovley. Cells were grown under strict anaerobic conditions at 30 °C in chemostats, as previously described (for more information see Esteve-Núñez, A., M. M. Rothermich, M. Sharma, and D. R. Lovley. 2004. Growth of Geobacter sulfurreducens under nutrient-limiting conditions in continuous culture. Environ. Microbiol.:in press.), with acetate (5 mM) as the electron donor and fumarate (27.5 mM) as the electron acceptor. For growth in the absence of fixed nitrogen, the ammonium chloride (4.7 mM) was omitted from the medium and fumarate served as the electron acceptor. Therefore, cultures with ammonium chloride were limited by acetate while cultures without ammonium chloride were limited by nitrogen. Cultures were maintained at a dilution rate of 0.05 h-1 for 5 culture vessel volumes to ensure that cells were at steady-state prior to harvesting. Cells were harvested by centrifugation at 4 °C and the cell pellet was flash-frozen in liquid nitrogen and then stored at -80 °C prior to RNA extraction. Cells grown in the absence of ammonium had acetylene reduction rates of 0.012 nmol/hr compared to 0.003 nmol/hr in ammonium-grown cells, providing evidence that these cells were fixing nitrogen.. The steady-state concentration of cells in the nitrogen-fixing chemostats (0.178 mg/mL + 0.011; mean + standard deviation, n=3) was significantly lower than chemostats provided with ammonium (0.45 mg/mL + 0.007). Three cultures of acetate limited growth with fumarate as the electron acceptor and three cultures of nitrogen limited growth with fumarate as the electron acceptor were grown. Each culture vessel was harvested and extracted for total RNA separately to produce three biological replicates for this experiment.

2005-01-01 | E-TIGR-82 | biostudies-arrayexpress

Gene expression in a Geobacter sulfurreducens strain adapted for faster Fe(III) oxide reduction grown with fumarate as an electron acceptor

2011-04-11 | E-GEOD-21313 | biostudies-arrayexpress

Transcription profiling of G sulfurreducens GGS Fe(III) vs fumarate

Project description:G. sulfurreducens (ATCC #51573) was obtained from the laboratory culture collection of Dr. Derek Lovley. Cells were grown under strict anaerobic conditions at 30 °C in chemostats, (see Esteve-Núñez, A., M. M. Rothermich, M. Sharma, and D. R. Lovley. 2004. Growth of Geobacter sulfurreducens under nutrient-limiting conditions in continuous culture. Environ. Microbiol.:in press. for more information), with acetate (5 mM) as the electron donor and Fe(III) citrate (55 mM) or fumarate (27.5 mM) as the electron acceptor. Under these conditions acetate is the substrate limiting growth. Cultures were maintained at a dilution rate of 0.05 h-1 for 5 culture vessel volumes to ensure that cells were at steady-state prior to harvesting. Cells were harvested by centrifugation at 4 °C and the cell pellet was flash-frozen in liquid nitrogen and then stored at 80 °C prior to RNA extraction. Three cultures of acetate limited growth with fumarate as the electron acceptor and three cultures of acetate limited growth with Fe(III) as the electron acceptor were grown. Each culture vessel was harvested and extracted for total RNA separately to produce three biological replicates for this experiment.

2005-01-01 | E-TIGR-81 | biostudies-arrayexpress

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