Ontology highlight
ABSTRACT:
PROVIDER: PRJNA663109 | ENA |
REPOSITORIES: ENA
Dataset's files
| Action | DRS | |||
|---|---|---|---|---|
| SRR12628837_1.fastq.gz | Fastqsanger.gz | |||
| SRR12628837_2.fastq.gz | Fastqsanger.gz | |||
| SRR12628838_1.fastq.gz | Fastqsanger.gz | |||
| SRR12628838_2.fastq.gz | Fastqsanger.gz | |||
| SRR12628839_1.fastq.gz | Fastqsanger.gz |
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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: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:Mesophilic elemental sulfur reduction at neutral to acidic pH
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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:Moderate-temperature extremely acidic ecosystem metagenome study
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Project description:Purpose: We aimed at i) obtaining insight into how a thermophile organism reacts to cold stress, and ii) evaluating the impact of HGT candidates on the acclimation process to temperature decrease. Methods: The experimental design followed a temperature shift timeline: after two weeks of cultivation at 42°C, constant illumination (90 μE) and constant shaking (160 rpm) in photoautotrophic conditions the first sampling took place (Hot_T48_1) and the cultures of G.sulphuraria were swiftly moved to 28°C ( = cold temperature). "Cold" samples were taken after 3h (Cold_T3_2), 12h (Cold_T12_3) and 48h (Cold_T48_4). After cold treatment at 28°C for 48 hours, the G. sulphuraria was then switched to 46°C for 48 hours (="Hot"). Again, samples were taken after 3h (Hot_T3_5), 12h (Hot_T12_6) and 48h (Hot_T48_7). Altogether, a 48h temperature timeshift at 28°C and successive recovery at 46°C were targeted for sampling. Results: Galdieria sulphuraria is a unicellular red alga that lives in hot, acidic, toxic metal-rich, volcanic environments, where few other organisms survive. Its genome harbours up to 5% of genes most likely acquired through horizontal gene transfer. These genes probably contributed to G. sulphuraria’s adaptation to its extreme habitats, resulting in today’s polyextremophilic traits. Here, we applied RNA-sequencing to obtain insights into the acclimation of a thermophilic organism towards temperatures below its growth optimum and to study how horizontally acquired genes contribute to cold acclimation. A decrease in growth temperature from 42 °C/46 °C to 28 °C resulted in an upregulation of ribosome biosynthesis, while excreted proteins, probably components of the cell wall, were downregulated. Photosynthesis was suppressed at cold temperatures, and transcript abundances indicated that C-metabolism switched from gluconeogenesis to glycogen degradation. Folate cycle and S-adenosylmethionine cycle (one-carbon metabolism) were transcriptionally upregulated, probably to drive the biosynthesis of betaine. All these cold-induced changes in gene expression were reversible upon temperature increase. Numerous genes acquired by horizontal gene transfer displayed pronounced temperature-dependent expression changes, corroborating the view that these genes contributed to adaptive evolution in G. sulphuraria.
2018-12-31 | GSE118890 | GEO
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.
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