Geobacter sulfurreducens
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ABSTRACT:
PROVIDER: PRJNA183870 | ENA |
REPOSITORIES: ENA
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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: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: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. Whole genome DNA microarray analysis was performed in order to determine which genes are up- or down-regulated in V1 compared to PCA, both grown with ferric citrate as an electron acceptor.
2011-04-12 | GSE21312 | GEO
Project description:Differential transcription of Geobacter sulfurreducens cells growing with Mn(IV) oxide or Fe(III) citrate provided as electron acceptor [Mn]
| PRJNA183871 | ENA
Project description:Whole-genome DNA microarray analysis of Geobacter sulfurreducens cells grown on Fe(III)-oxide or Mn(IV)-oxide versus cells grown on soluble Fe(III) citrate indicated that there were significant differences in transcription patterns during growth on the insoluble metal oxides compared to growth on soluble Fe(III). Many of the genes that appeared to be up-regulated during growth on the metal hydroxides were involved in electron transport. The most highly up-regulated genes for both conditions were omcS and omcT, which encode co-transcribed c-type cytochromes exposed on the outer surface of the cell that are known to be required for Fe(III) and Mn(IV)-oxide reduction. Other electron transport genes that were up-regulated on both insoluble metals included the gene coding for the outer membrane c-type cytochrome, OmcG, genes for the outer membrane proteins, OmpB and OmpC, and the gene that codes for the structural protein of electrically conductive pili, PilA. Genes that were up-regulated in cells grown on Fe(III)-oxide but not Mn(IV)-oxide, included outer membrane c-type cytochromes including OmcE, a putative DMSO reductase protein, and proteins from the cytochrome bc1 complex. Electron transport genes that were only up-regulated in Mn(IV)-oxide grown cells included the genes that code for the outer membrane c-type cytochromes, OmcZ and OmcB, the periplasmic c-type cytochrome, MacA, and fumarate reductase. Genetic studies indicated that the c-type cytochrome proteins, PpcH, OmcJ, OmcM, OmcV, MacA, OmcF, OmcI, and OmcQ, and the iron sulfur subunit of the cytochrome b/b6 complex, QcrA, are important for reduction of insoluble Fe(III)-oxides but do not appear to be important for Mn(IV) reduction. These results demonstrate that the physiology of Fe(III) reducing bacteria differ significantly during growth on insoluble electron and soluble electron acceptors and emphasizes the importance of c-type cytochromes in extracellular electron transfer in G. sulfurreducens. Geobacter sulfurreducens cells were grown with acetate (5 mM) provided as the electron donor and either Fe(III) oxide or Fe(III) citrate provided as the electron acceptor. Cells were harvested at mid-log and total RNA was extracted. Total RNA (0.5 M-NM-<g) was amplified using the MessageAmp II-Bacteria Kit (Ambion, Foster City, CA) according to the manufacturers instructions. Ten micrograms of amplified RNA (aRNA) was chemically labeled with Cy3 (for the control or soluble electron acceptor condition) or Cy5 (for the experimental or insoluble electron acceptor condition) dye using the MicroMax ASAP RNA Labeling Kit (Perkin Elmer, Wellesley, MA) according to the manufacturerM-bM-^@M-^Ys instructions. RNA samples from three biological replicates were hybridized in duplicate on 12K Combimatrix antisense-detecting arrays. The experimental condition (DL1 grown with Fe(III) oxide as acceptor) was labeled with cy5, the control condition (DL1 grown with Fe(III) citrate as acceptor) was labeled with cy3
2012-12-15 | E-GEOD-42918 | biostudies-arrayexpress
Project description:Whole-genome DNA microarray analysis of Geobacter sulfurreducens cells grown on Fe(III)-oxide or Mn(IV)-oxide versus cells grown on soluble Fe(III) citrate indicated that there were significant differences in transcription patterns during growth on the insoluble metal oxides compared to growth on soluble Fe(III). Many of the genes that appeared to be up-regulated during growth on the metal hydroxides were involved in electron transport. The most highly up-regulated genes for both conditions were omcS and omcT, which encode co-transcribed c-type cytochromes exposed on the outer surface of the cell that are known to be required for Fe(III) and Mn(IV)-oxide reduction. Other electron transport genes that were up-regulated on both insoluble metals included the gene coding for the outer membrane c-type cytochrome, OmcG, genes for the outer membrane proteins, OmpB and OmpC, and the gene that codes for the structural protein of electrically conductive pili, PilA. Genes that were up-regulated in cells grown on Fe(III)-oxide but not Mn(IV)-oxide, included outer membrane c-type cytochromes including OmcE, a putative DMSO reductase protein, and proteins from the cytochrome bc1 complex. Electron transport genes that were only up-regulated in Mn(IV)-oxide grown cells included the genes that code for the outer membrane c-type cytochromes, OmcZ and OmcB, the periplasmic c-type cytochrome, MacA, and fumarate reductase. Genetic studies indicated that the c-type cytochrome proteins, PpcH, OmcJ, OmcM, OmcV, MacA, OmcF, OmcI, and OmcQ, and the iron sulfur subunit of the cytochrome b/b6 complex, QcrA, are important for reduction of insoluble Fe(III)-oxides but do not appear to be important for Mn(IV) reduction. These results demonstrate that the physiology of Fe(III) reducing bacteria differ significantly during growth on insoluble electron and soluble electron acceptors and emphasizes the importance of c-type cytochromes in extracellular electron transfer in G. sulfurreducens. Geobacter sulfurreducens cells were grown with acetate (5 mM) provided as the electron donor and either Fe(III) oxide or Fe(III) citrate provided as the electron acceptor. Cells were harvested at mid-log and total RNA was extracted. Total RNA (0.5 M-NM-<g) was amplified using the MessageAmp II-Bacteria Kit (Ambion, Foster City, CA) according to the manufacturers instructions. Ten micrograms of amplified RNA (aRNA) was chemically labeled with Cy3 (for the control or soluble electron acceptor condition) or Cy5 (for the experimental or insoluble electron acceptor condition) dye using the MicroMax ASAP RNA Labeling Kit (Perkin Elmer, Wellesley, MA) according to the manufacturerM-bM-^@M-^Ys instructions. RNA samples from three biological replicates were hybridized in duplicate on 12K Combimatrix antisense-detecting arrays. The experimental condition (DL1 grown with Mn(IV) oxide as acceptor) was labeled with cy5, the control condition (DL1 grown with Fe(III) citrate as acceptor) was labeled with cy3
2012-12-15 | E-GEOD-42919 | biostudies-arrayexpress
Project description:Whole-genome DNA microarray analysis of Geobacter sulfurreducens cells grown on Fe(III)-oxide or Mn(IV)-oxide versus cells grown on soluble Fe(III) citrate indicated that there were significant differences in transcription patterns during growth on the insoluble metal oxides compared to growth on soluble Fe(III). Many of the genes that appeared to be up-regulated during growth on the metal hydroxides were involved in electron transport. The most highly up-regulated genes for both conditions were omcS and omcT, which encode co-transcribed c-type cytochromes exposed on the outer surface of the cell that are known to be required for Fe(III) and Mn(IV)-oxide reduction. Other electron transport genes that were up-regulated on both insoluble metals included the gene coding for the outer membrane c-type cytochrome, OmcG, genes for the outer membrane proteins, OmpB and OmpC, and the gene that codes for the structural protein of electrically conductive pili, PilA. Genes that were up-regulated in cells grown on Fe(III)-oxide but not Mn(IV)-oxide, included outer membrane c-type cytochromes including OmcE, a putative DMSO reductase protein, and proteins from the cytochrome bc1 complex. Electron transport genes that were only up-regulated in Mn(IV)-oxide grown cells included the genes that code for the outer membrane c-type cytochromes, OmcZ and OmcB, the periplasmic c-type cytochrome, MacA, and fumarate reductase. Genetic studies indicated that the c-type cytochrome proteins, PpcH, OmcJ, OmcM, OmcV, MacA, OmcF, OmcI, and OmcQ, and the iron sulfur subunit of the cytochrome b/b6 complex, QcrA, are important for reduction of insoluble Fe(III)-oxides but do not appear to be important for Mn(IV) reduction. These results demonstrate that the physiology of Fe(III) reducing bacteria differ significantly during growth on insoluble electron and soluble electron acceptors and emphasizes the importance of c-type cytochromes in extracellular electron transfer in G. sulfurreducens. Geobacter sulfurreducens cells were grown with acetate (5 mM) provided as the electron donor and either Fe(III) oxide or Fe(III) citrate provided as the electron acceptor. Cells were harvested at mid-log and total RNA was extracted. Total RNA (0.5 μg) was amplified using the MessageAmp II-Bacteria Kit (Ambion, Foster City, CA) according to the manufacturers instructions. Ten micrograms of amplified RNA (aRNA) was chemically labeled with Cy3 (for the control or soluble electron acceptor condition) or Cy5 (for the experimental or insoluble electron acceptor condition) dye using the MicroMax ASAP RNA Labeling Kit (Perkin Elmer, Wellesley, MA) according to the manufacturer’s instructions.
2012-12-15 | GSE42919 | GEO
Project description:Whole-genome DNA microarray analysis of Geobacter sulfurreducens cells grown on Fe(III)-oxide or Mn(IV)-oxide versus cells grown on soluble Fe(III) citrate indicated that there were significant differences in transcription patterns during growth on the insoluble metal oxides compared to growth on soluble Fe(III). Many of the genes that appeared to be up-regulated during growth on the metal hydroxides were involved in electron transport. The most highly up-regulated genes for both conditions were omcS and omcT, which encode co-transcribed c-type cytochromes exposed on the outer surface of the cell that are known to be required for Fe(III) and Mn(IV)-oxide reduction. Other electron transport genes that were up-regulated on both insoluble metals included the gene coding for the outer membrane c-type cytochrome, OmcG, genes for the outer membrane proteins, OmpB and OmpC, and the gene that codes for the structural protein of electrically conductive pili, PilA. Genes that were up-regulated in cells grown on Fe(III)-oxide but not Mn(IV)-oxide, included outer membrane c-type cytochromes including OmcE, a putative DMSO reductase protein, and proteins from the cytochrome bc1 complex. Electron transport genes that were only up-regulated in Mn(IV)-oxide grown cells included the genes that code for the outer membrane c-type cytochromes, OmcZ and OmcB, the periplasmic c-type cytochrome, MacA, and fumarate reductase. Genetic studies indicated that the c-type cytochrome proteins, PpcH, OmcJ, OmcM, OmcV, MacA, OmcF, OmcI, and OmcQ, and the iron sulfur subunit of the cytochrome b/b6 complex, QcrA, are important for reduction of insoluble Fe(III)-oxides but do not appear to be important for Mn(IV) reduction. These results demonstrate that the physiology of Fe(III) reducing bacteria differ significantly during growth on insoluble electron and soluble electron acceptors and emphasizes the importance of c-type cytochromes in extracellular electron transfer in G. sulfurreducens. Geobacter sulfurreducens cells were grown with acetate (5 mM) provided as the electron donor and either Fe(III) oxide or Fe(III) citrate provided as the electron acceptor. Cells were harvested at mid-log and total RNA was extracted. Total RNA (0.5 μg) was amplified using the MessageAmp II-Bacteria Kit (Ambion, Foster City, CA) according to the manufacturers instructions. Ten micrograms of amplified RNA (aRNA) was chemically labeled with Cy3 (for the control or soluble electron acceptor condition) or Cy5 (for the experimental or insoluble electron acceptor condition) dye using the MicroMax ASAP RNA Labeling Kit (Perkin Elmer, Wellesley, MA) according to the manufacturer’s instructions.
2012-12-15 | GSE42918 | GEO
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: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.
2013-02-18 | GSE40316 | GEO