Browse
Submit Data
Databases
API
Help

Dataset Information

0 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

Analysis of Gene Expression Under Nitrogen Fixing Conditions in Geobacter sulfurreducens

ABSTRACT: In this study, expression analysis using electrochemically synthesized Combimatrix 12K DNA microarrays was validated in G sulfurreducens. Growth under nitrogen fixing conditions and growth in ammonium amended medium, respectively, were the experimental and control conditions. Expression analysis using this platform was also compared to expression analysis on whole cDNA microarrays. Keywords: two-condition comparison

ORGANISM(S): Geobacter sulfurreducens

PROVIDER: GSE7147 | GEO | 2007/08/01

SECONDARY ACCESSION(S): PRJNA98189

REPOSITORIES: GEO

ACCESS DATA

Json Xml

Similar Datasets

Adaptation of Geobacter sulfurreducens to Overcome the Loss of a Key Periplasmic c-Type Cytochrome

Project description:ppcA is a member of a family of small, periplamic c-type cytochromes in Geobact sulfurreducens. The ppcA mutant displays displays a growth defect on ferric citrate medium, but the mutant has been adapted to grow to near wild-type levels on ferric citrate. The aim of this study was to elucidate gene expression changes responsible for this adaptive growth. Keywords: cell type comparison Three biological replicates were hybridized in duplicate on 12K Combimatrix sense-detecting arrays, the experiment (ppcA mutant) was labeled with Cy5, and the control (wildtype) was labeled with Cy3.

2010-07-21 | E-GEOD-7356 | biostudies-arrayexpress

Geobacter sulfurreducens

Project description:Analysis of Gene Expression Under Nitrogen Fixing Conditions in Geobacter sulfurreducens

| PRJNA98189 | ENA

Nitrate reduction by Geobacter sulfurreducens and the catalytic role of palladium on the reduction pathway

Project description:Geobacter sulfurreducens is a widely explored microorganism recognized by its metabolic versatility able to reduce a number of external electron acceptors. In the present study the capacity of this strain to reduce nitrate was evaluated along with its transcriptomic profile under nitrate-reducing conditions and the catalytic role of Pd nanoparticles on the reductive pathway. Results demonstrated that G. sulfurreducens was able to reduce nitrate and important kinetic differences related to the time response were found among the electron donors used (acetate and hydrogen). When using acetate, a delay response on nitrate reduction of 4 days and reduction of 94% of nitrate was achieved, while nitrite was not detected, and all the nitrogen was recovered as ammonium (79.6 ± 5.7 %). The use of hydrogen as electron donor increased 2-fold the maximum rate of nitrate reduction, leading to 93% reduction of nitrate during the first 20 h with recovery of 45% as ammonium, while nitrite was not detected. In addition, transcriptome profiling analysis of G. sulfurreducens under nitrate-reducing conditions using hydrogen or acetate as an electron donor at 2 and 6 days reveals that a core of 146 genes (69 upregulated and 77 downregulated) are differentially expressed in all conditions. Genes related to nitrogen metabolism, such as nrfA and nrfH, gdhA, and amtB, were upregulated in the incubations and RT-qPCR data confirmed upregulations of these genes. Experiments performed with biologically synthesized Pd (Bio-Pd) + G. sulfurreducens cells demonstrated synergistic input of Bio-Pd and the metabolic capacity of G. sulfurreducens. These results expand the metabolic versatility of G. sulfurreducens, which may have important implications in nitrogen cycling in natural environments and engineered systems.

2023-06-01 | GSE179298 | GEO

Protein validation of Geobacter Sulfurreducens

Project description:Protein validation of Geobacter Sulfurreducens using LC-MS/MS

2014-03-20 | PXD000854 | Pride

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

Geobacter sulfurreducens

Project description:Geobacter sulfurreducens Raw sequence reads

| PRJNA675673 | ENA

Geobacter sulfurreducens biofilm iTRAQ analysis

Project description:Geobacter sulfurreducens is a dissimilatory metal-reducing bacterium capable of forming thick electron-conducting biofilms on solid electrodes in the absence of alternative electron acceptors. The remarkable ability of such biofilms to transfer electrons, liberated from soluble organic electron donors, over long distances has attracted scientific interest as to the mechanism for this process, and technological interest for application to microbial fuel and electrolysis cells and sensors. Here, we employ comparative proteomics to identify key metabolic pathways involved in G. sulfurreducens respiration by planktonic cells versus electron-conducting biofilms, in an effort to elucidate long-range electron transfer mechanisms.

2018-02-16 | PXD002667 | Pride

Geobacter sulfurreducens

Project description:Geobacter sulfurreducens Genome sequencing and assembly

| PRJNA694193 | ENA

Geobacter sulfurreducens and Pseudomonas aeruginosa adapted cocultures SWATH-MS

Project description:In this study we further investigate the previously observed syntrophic interaction between Geobacter sulfurreducens and Pseudomonas aeruginosa. In early coculture establishment, two genetic variants of G. sulfurreducens emerged that were strongly selected for throughout coculture evolution. Single nucleotide polymorphism (SNP) variants occurred in fabI and tetR genes of G. sulfurreducens. The tetR variants displayed upregulation of adenylate cyclase transporter, CyaE and of RND efflux pump proteins as determined through SWATH-MS proteomics.

2020-04-20 | PXD013990 | Pride

Geobacter sulfurreducens KN400

Project description:Geobacter sulfurreducens KN400 Genome sequencing

| PRJNA39745 | ENA