Plant growth promoting arylsulfatase producing bacteria
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ABSTRACT:
PROVIDER: PRJEB28499 | ENA |
REPOSITORIES: ENA
Similar Datasets
Project description:Thermococcus kodakarensis preferentially utilizes amino acids as carbon and energy sources in the presence of elemental sulfur as a terminal electron acceptor, while it can assimilate and grow on starch or pyruvate using proton as a terminal acceptor, generating hydrogen in the absence of elemental sulfur. SurR is a transcriptional regulator controlling hydrogen and elemental sulfur metabolism. To identify the genes that are under the regulation of Tk-SurR, we investigated the transcriptional profiling of Tk-SurR deletion strain grown in the presence of elemental sulfur at 85ËC by comparing with the host strain, KU216. One-condition experiment, KU216 vs. DTS cells. Technical replicates: 2 DTS grown in the presence of elemental sulfur at 85ËC, independently measured. One replicate per array.
2016-07-03 | E-GEOD-71984 | biostudies-arrayexpress
Project description:Thermococcus kodakarensis preferentially utilizes amino acids as carbon and energy sources in the presence of elemental sulfur as a terminal electron acceptor, while it can assimilate and grow on starch or pyruvate using proton as a terminal acceptor, generating hydrogen in the absence of elemental sulfur. SurR is a transcriptional regulator controlling hydrogen and elemental sulfur metabolism. To identify the genes that are under the regulation of Tk-SurR, we investigated the transcriptional profiling of Tk-SurR deletion strain grown in the presence of elemental sulfur at 85˚C by comparing with the host strain, KU216.
2016-01-01 | GSE71984 | GEO
Project description:Desulfurella amilsii is an acidotolerant sulfur-reducing bacterium isolated from sediments of an acidic river. It can grow in a broad range of pH and can obtain energy via respiring elemental sulfur or thiosulfate, as well as by disproportionating elemental sulfur. Its genome encodes the enzyme sulfur reductase, and several rhodanese-like proteins, possibly playing a role in sulfur respiration and disproportionation. Thiosulfate reductase and dissimilatory sulfite reductase are encoded and might play a role during the respiration of thiosulfate. The involvement of these enzymes in the reductive routes of sulfur metabolism is not yet clearly understood. Desulfurella amilsii was used in this study to combine strategies for sulfur metabolism research on the protein level to shed some light on the pathways involved in the metabolism of this microorganism.
2018-10-19 | PXD008496 | Pride
Project description:The purple sulfur bacterium Allochromatium vinosum DSM 180T is one of the best studied sulfur-oxidizing anoxygenic phototrophic bacteria and has been developed into a model organism for laboratory-based studies of oxidative sulfur metabolism. Here, we took advantage of the organismM-bM-^@M-^Ys high metabolic versatility and performed whole-genome transcriptional profiling to investigate the response of A. vinosum cells upon exposure to sulfide, thiosulfate, elemental sulfur or sulfite as compared to photoorganoheterotrophic growth on malate. Differential expression (at least twofold) of 1149 genes was observed, corresponding to 30% of the A. vinosum genome. A total of 549 genes were identified for which relative transcription increased at least twofold during growth on one of the different sulfur sources while relative transcription of 599 genes decreased. A significant number of genes that were strongly induced have documented sulfur-metabolism-related functions. Among these are the dsr genes including dsrAB for dissimilatory sulfite reductase and the sgp genes for the proteins of the sulfur globule envelope thus confirming former results. In addition we were able to identify new genes encoding proteins with appropriate subcellular localization and properties to participate in oxidative dissimilatory sulfur metabolism. Two of these were chosen for inactivation and phenotypic analyses of the respective mutant strains. This approach verified the importance of the encoded proteins for the oxidation of sulfide and thereby also documented the suitability of comparative transcriptomics for the identification of new sulfur-related genes in anoxygenic phototrophic sulfur bacteria. In this study, the relative genomic expression profiles of A. vinosum DSM 180T growing photolithoautotrophically on different reduced sulfur compounds were determined in comparison to those of cells grown photoorganoheterothrophically on malate (RCV medium) at exactly the same light intensity. The malate-containing medium was supplied with 0.815 mM sulfate in order to satisfy the sulfur-requirement for biosynthesis of sulfur-containing cell constituents. Three independent photolithoautotrophic cultures each, grown on sulfide, thiosulfate or sulfite were harvested 1 h, 2 h or 7 h, respectively, after inoculation. When elemental sulfur was the substrate, four independent cultures were harvested 3 h after inoculation.
2013-07-29 | E-GEOD-44040 | biostudies-arrayexpress
Project description:The purple sulfur bacterium Allochromatium vinosum DSM 180T is one of the best studied sulfur-oxidizing anoxygenic phototrophic bacteria and has been developed into a model organism for laboratory-based studies of oxidative sulfur metabolism. Here, we took advantage of the organismM-bM-^@M-^Ys high metabolic versatility and performed whole-genome transcriptional profiling to investigate the response of A. vinosum cells upon exposure to sulfide, thiosulfate, elemental sulfur or sulfite as compared to photoorganoheterotrophic growth on malate. Differential expression (at least twofold) of 1149 genes was observed, corresponding to 30% of the A. vinosum genome. A total of 549 genes were identified for which relative transcription increased at least twofold during growth on one of the different sulfur sources while relative transcription of 599 genes decreased. A significant number of genes that were strongly induced have documented sulfur-metabolism-related functions. Among these are the dsr genes including dsrAB for dissimilatory sulfite reductase and the sgp genes for the proteins of the sulfur globule envelope thus confirming former results. In addition we were able to identify new genes encoding proteins with appropriate subcellular localization and properties to participate in oxidative dissimilatory sulfur metabolism. Two of these were chosen for inactivation and phenotypic analyses of the respective mutant strains. This approach verified the importance of the encoded proteins for the oxidation of sulfide and thereby also documented the suitability of comparative transcriptomics for the identification of new sulfur-related genes in anoxygenic phototrophic sulfur bacteria. In this study, the relative genomic expression profiles of A. vinosum DSM 180T growing photolithoautotrophically on different reduced sulfur compounds were determined in comparison to those of cells grown photoorganoheterothrophically on malate (RCV medium) at exactly the same light intensity. The malate-containing medium was supplied with 0.815 mM sulfate in order to satisfy the sulfur-requirement for biosynthesis of sulfur-containing cell constituents. Three independent photolithoautotrophic cultures each, grown on sulfide, thiosulfate or sulfite were harvested 1 h, 2 h or 7 h, respectively, after inoculation. When elemental sulfur was the substrate, four independent cultures were harvested 3 h after inoculation.
2013-07-29 | E-GEOD-44041 | biostudies-arrayexpress
Project description:The Chlamydomonas reinhardtii transcription factor PSR1 is required for the control of activities involved in scavenging phosphate from the environment during periods of phosphorus limitation. Increased scavenging activity reflects the development of high-affinity phosphate transport and the expression of extracellular phosphatases that can cleave phosphate from organic compounds in the environment. A comparison of gene expression patterns using microarray analyses and quantitative PCRs with wild-type and psr1 mutant cells deprived of phosphorus has revealed that PSR1 also controls genes encoding proteins with potential "electron valve" functions--these proteins can serve as alternative electron acceptors that help prevent photodamage caused by overexcitation of the photosynthetic electron transport system. In accordance with this finding, phosphorus-starved psr1 mutants die when subjected to elevated light intensities; at these intensities, the wild-type cells still exhibit rapid growth. Acclimation to phosphorus deprivation also involves a reduction in the levels of transcripts encoding proteins involved in photosynthesis and both cytoplasmic and chloroplast translation as well as an increase in the levels of transcripts encoding stress-associated chaperones and proteases. Surprisingly, phosphorus-deficient psr1 cells (but not wild-type cells) also display expression patterns associated with specific responses to sulfur deprivation, suggesting a hitherto unsuspected link between the signal transduction pathways involved in controlling phosphorus and sulfur starvation responses. Together, these results demonstrate that PSR1 is critical for the survival of cells under conditions of suboptimal phosphorus availability and that it plays a key role in controlling both scavenging responses and the ability of the cell to manage excess absorbed excitation energy. Set of arrays that are part of repeated experiments Biological Replicate Computed
2006-08-18 | E-GEOD-4568 | biostudies-arrayexpress
Project description:S. cerevisiae strain FY1679 homozygous for HO deletion by KanMX4 was grown in a series of nutrient limited continuous cultures carbon, nitrogen, phosphorus and sulfur limitation to determine genes which are growth rate regulated and those which are nutrient specific regulated.
2007-05-02 | E-MEXP-115 | biostudies-arrayexpress
Project description:<p>Sulfur (S) is a major heteroatom in organic matter. This project evaluated spatial variability in the concentration and molecular-level composition of organic sulfur along gradients of depth and latitude. We measured the concentration of total organic sulfur (TOS) directly from whole seawater. Our data reveal high variability in organic sulfur, relative to established variability in total organic carbon or nitrogen. The deep ocean contained significant amounts of organic sulfur, and the concentration of TOS in North Atlantic Deep Water (NADW) decreased with increasing age while total organic carbon remained stable. Analysis of dissolved organic matter extracts by ultrahigh resolution mass spectrometry revealed that 6% of elemental formulas contained sulfur. The sulfur-containing compounds were structurally diverse, and showed higher numbers of sulfur-containing elemental formulas as NADW moved southward. These measurements of organic sulfur in seawater provide the foundation needed to define the factors controlling organic sulfur in the global ocean.</p>
2019-11-12 | MTBLS1024 | MetaboLights
Project description:We used the previously designed oligonucleotide-based microarray (Burgmann et al. Environmental Microbiology 2007, 9: 2742-2755) to detect the transcripts of R. pomeroyi DSS-3 genes when the cells were cultured under steady-state carbon (glucose), nitrogen (ammonium), phosphorus (phosphate), or sulfur (sulfate) limitation.
2011-10-01 | GSE27032 | GEO
Project description:The Chlamydomonas reinhardtii transcription factor PSR1 is required for the control of activities involved in scavenging phosphate from the environment during periods of phosphorus limitation. Increased scavenging activity reflects the development of high-affinity phosphate transport and the expression of extracellular phosphatases that can cleave phosphate from organic compounds in the environment. A comparison of gene expression patterns using microarray analyses and quantitative PCRs with wild-type and psr1 mutant cells deprived of phosphorus has revealed that PSR1 also controls genes encoding proteins with potential "electron valve" functions--these proteins can serve as alternative electron acceptors that help prevent photodamage caused by overexcitation of the photosynthetic electron transport system. In accordance with this finding, phosphorus-starved psr1 mutants die when subjected to elevated light intensities; at these intensities, the wild-type cells still exhibit rapid growth. Acclimation to phosphorus deprivation also involves a reduction in the levels of transcripts encoding proteins involved in photosynthesis and both cytoplasmic and chloroplast translation as well as an increase in the levels of transcripts encoding stress-associated chaperones and proteases. Surprisingly, phosphorus-deficient psr1 cells (but not wild-type cells) also display expression patterns associated with specific responses to sulfur deprivation, suggesting a hitherto unsuspected link between the signal transduction pathways involved in controlling phosphorus and sulfur starvation responses. Together, these results demonstrate that PSR1 is critical for the survival of cells under conditions of suboptimal phosphorus availability and that it plays a key role in controlling both scavenging responses and the ability of the cell to manage excess absorbed excitation energy. Set of arrays that are part of repeated experiments Keywords: Biological Replicate
2006-08-18 | GSE4568 | GEO