Sulfolobus acidocaldarius
Ontology highlight
ABSTRACT:
PROVIDER: PRJNA35727 | ENA |
REPOSITORIES: ENA
Dataset's files
| Action | DRS | |||
|---|---|---|---|---|
| Other | ||||
| SRR5241990.fastq.gz | Fastqsanger.gz | |||
| SRR5241991.fastq.gz | Fastqsanger.gz | |||
| SRR5241992.fastq.gz | Fastqsanger.gz | |||
| SRR5503851.fastq.gz | Fastqsanger.gz |
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Similar Datasets
Project description:Extreme thermoacidophilic sulfur-oxidizing archaeon
| PRJNA13935 | ENA
Project description:(from abstract): Iron oxidation is a desirable trait of biomining microorganisms, although the mechanism is not well-understood in extreme thermoacidophiles. The complete genome sequence of the extremely thermoacidophilic archaeon Metallosphaera sedula DSM 5348 (2.2 Mb, ~2300 ORFs) provides insights into biologically catalyzed metal sulfide oxidation. Comparative genomics was used to identify pathways and proteins (in)directly involved with bioleaching. As expected, the M. sedula genome encodes genes related to autotrophic carbon fixation, metal tolerance, and adhesion. Also, terminal oxidase cluster organization indicates the presence of hybrid quinol-cytochrome oxidase complexes. Comparisons with the mesophilic biomining bacterium Acidithiobacillus ferrooxidans ATCC 23270 indicate that the M. sedula genome encodes at least one putative rusticyanin, involved in iron oxidation. The fox gene cluster, involved in iron oxidation in the thermoacidophilic archaeon Sulfolobus metallicus, could also be identified. These iron-oxidizing components are missing from genomes of non-leaching Sulfolobales like Sulfolobus solfataricus P2 and Sulfolobus acidocaldarius DSM 639. Whole genome transcriptional response analysis showed that 88 ORFs were up-regulated 2-fold or more in M. sedula upon addition of ferrous sulfate to yeast extract-based medium; these included components of terminal oxidase clusters predicted to be involved with iron oxidation, as well as genes predicted to be involved with sulfur metabolism. Many hypothetical proteins were also differentially transcribed, indicating that aspects of the iron and sulfur metabolism of M. sedula remain to be identified and characterized. Keywords: substrate response
2008-05-02 | GSE11296 | GEO
Project description:(from abstract): Iron oxidation is a desirable trait of biomining microorganisms, although the mechanism is not well-understood in extreme thermoacidophiles. The complete genome sequence of the extremely thermoacidophilic archaeon Metallosphaera sedula DSM 5348 (2.2 Mb, ~2300 ORFs) provides insights into biologically catalyzed metal sulfide oxidation. Comparative genomics was used to identify pathways and proteins (in)directly involved with bioleaching. As expected, the M. sedula genome encodes genes related to autotrophic carbon fixation, metal tolerance, and adhesion. Also, terminal oxidase cluster organization indicates the presence of hybrid quinol-cytochrome oxidase complexes. Comparisons with the mesophilic biomining bacterium Acidithiobacillus ferrooxidans ATCC 23270 indicate that the M. sedula genome encodes at least one putative rusticyanin, involved in iron oxidation. The fox gene cluster, involved in iron oxidation in the thermoacidophilic archaeon Sulfolobus metallicus, could also be identified. These iron-oxidizing components are missing from genomes of non-leaching Sulfolobales like Sulfolobus solfataricus P2 and Sulfolobus acidocaldarius DSM 639. Whole genome transcriptional response analysis showed that 88 ORFs were up-regulated 2-fold or more in M. sedula upon addition of ferrous sulfate to yeast extract-based medium; these included components of terminal oxidase clusters predicted to be involved with iron oxidation, as well as genes predicted to be involved with sulfur metabolism. Many hypothetical proteins were also differentially transcribed, indicating that aspects of the iron and sulfur metabolism of M. sedula remain to be identified and characterized. Dye flip of Mse cells includes two samples, yeast exact (YE) and yeast extract + ferrous sulfate (YEF). The first slide, Y3F5, has YE RNA labeled with cy3 and YEF RNA labeled with cy5, while the second slide, F3Y5, has YEF RNA labeled with cy3 and YE RNA labeled with cy5. YE serves as the reference condition, with the expectation that ORFs involved with Fe2+ oxidation (and SO4 metabolism) will be upregulated on YEF (log2 fold change of YE-YEF < -1).
2008-05-02 | E-GEOD-11296 | biostudies-arrayexpress
Project description:This study provides novel insights into archaeal stress response. The effect of nutrient limitation on the thermoacidophilic crenarchaeon Sulfolobus acidocaldarius was monitored over time on transcriptomic, proteomic and metabolic level. To our knowledge, this linkage of transcriptome, proteome, metabolome analysis makes this study a pioneer study to elucidate cellular stress response triggered by nutrient limitation. We further connect previously identified pH and salt stress responsive genes (1) with genes regulated in starvation and suggest that they constitute the core of stress responsive genes active under multiple stress sources.
2018-12-21 | GSE113716 | GEO
Project description:Sulfur-oxidizing extreme halophile
| PRJNA15767 | ENA
Project description:To study the cellular global response of the thermoacidophilic Archaeon Sulfolobus acidocaldarius upon solvent exposure we performed transcriptome comparing the response of planktonic and biofilm cells in absence and presence 1-butanol. S. acidocaldarius was grown in Petri dishes (static incubation) in the absence and presence of 0.5% and 1% (v/v) 1-butanol at 76°C for four days. Planktonic and biofilm cells were harvested and the transcriptional response towards 1-butanol was analysed via RNA-seq. In detail:Biofilm and planktonic cell samples (supernatant after static incubation) were generated in Petri dishes (92 x 16 mm, Polystyrene, without cams, Sarstedt) as described before. Cells grown under six different conditions, including Biofilm-Control (BF0), Biofilm-0.5% (v/v) 1-Butanol (BF05), Biofilm-1% (v/v) 1-Butanol (BF1), Planktonic-Control (PL0), Planktonic-0.5% (v/v) 1-Butanol (PL05), Planktonic-1% (v/v) 1-Butanol (PL1), were seperated, harvested by centrifugation (10 min, 5,000 x g, 4 °C) and immediately frozen at -70 °C. Isolation of cells was performed in triplicates with ten technical replicas each. Samples were pooled to obtain sufficient cell mass for further processing. RNA was isolated using Trizol (Thermo Fisher Scientific). In accordance, sequencing libraries were prepared via Illumina TruSeq stranded mRNA using Ribozero for RNA depletion. Sequencing was performed on a MiSeq instrument (Illumina, San Diego, California, USA) using v3 chemistry with a read length of 2x76 nt.
2021-02-20 | E-MTAB-10093 | biostudies-arrayexpress
Project description:Small RNAs and L7Ae co-immunoprecipitated RNA were isolated from the thermophilic archaeon Sulfolobus acidocaldarius and subjected to Illumina sequencing. The sRNome revealed a high abundance of C/D box sRNAs and CRISPR RNAs. The L7Ae-RNA interactome showed enrichment of all known interactors of the L7Ae protein, i.e. C/D box sRNAs, H/ACA box sRNAs, RNaseP, rRNA. A high abundance of reads for the SRP RNA was found, suggesting L7Ae´s interaction with this universal RNA. Many mRNA reads were enriched, several of them comprise binding sites for the L7Ae protein.
2017-02-10 | GSE94748 | GEO
Project description:The UDP-sulfoquinovose synthase Agl3 from Sulfolobus acidocaldarius converts UDP-D-glucose and sulfite to UDP-sulfoquinovose, the activated form of sulfoquinovose required for its incorporation into glycoconjugates. Based on the amino acid sequence, Agl3 belongs to the short-chain dehydrogenase/reductase enzyme superfamily, together with SQD1 from Arabidopsis thaliana, the only UDP-sulfoquinovose synthase with known crystal structure. By comparison of sequence and structure of Agl3 and SQD1, putative catalytic amino acids of Agl3 were selected for mutational analysis. The obtained data suggest for Agl3 a modified dehydratase reaction mechanism. We propose that in vitro biosynthesis of UDP-sulfoquinovose occurs through an NAD(+)-dependent oxidation/dehydration/enolization/sulfite addition process. In the absence of a sulfur donor, UDP-D-glucose is converted via UDP-4-keto-D-glucose to UDP-D-glucose-5,6-ene, the structure of which was determined by (1)H and (13)C-NMR spectroscopy. During the redox reaction the cofactor remains tightly bound to Agl3 and participates in the reaction in a concentration-dependent manner. For the first time, the rapid initial electron transfer between UDP-D-glucose and NAD(+) could be monitored in a UDP-sulfoquinovose synthase. Deuterium labeling confirmed that dehydration of UDP-D-glucose occurs only from the enol form of UDP-4-keto-glucose. The obtained functional data are compared with those from other UDP-sulfoquinovose synthases. A divergent evolution of Agl3 from S. acidocaldarius is suggested.
| S-EPMC4388408 | biostudies-literature