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RNA-seq of thermoacidophilic crenarchaeon Sulfolobus acidocaldarius grwon with different glycerol concentrations reveals an unusual glycerol-3-phosphate dehydrogenase

ABSTRACT: RNA-seq of thermoacidophilic crenarchaeon Sulfolobus acidocaldarius grwon with different glycerol concentrations reveals an unusual glycerol-3-phosphate dehydrogenase

PROVIDER: PRJEB78563 | ENA |

REPOSITORIES: ENA

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			Action	DRS
	ERR13437825_1.fastq.gz	Fastqsanger.gz
	ERR13437825_2.fastq.gz	Fastqsanger.gz
	ERR13437826_1.fastq.gz	Fastqsanger.gz
	ERR13437826_2.fastq.gz	Fastqsanger.gz
	ERR13437827_1.fastq.gz	Fastqsanger.gz

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RNA-seq of thermoacidophilic crenarchaeon Sulfolobus acidocaldarius grwon with different glycerol concentrations reveals an unusual glycerol-3-phosphate dehydrogenase

Project description:To elucidate the glycerol catabolism in glycerol-adapted S. acidocaldarius MW00G the carbon source dependent global transcriptional response to glycerol compared to D-xylose the transcriptome was analyzed via RNA-Seq. Growth experiments with the S. acidocaldarius MW00G werewas performed in triplicates at 76°C and 120 rpm under constant shaking using (Innova®44, (New Brunswick, Germany) in the presence 10 mM glycerol, 20 mM glycerol or 40 mM glycerol as sole carbon and energy source. For comparison the same strain was cultivated with 0.2 % (w/v) D-xylose. RNA isolation, library preparation, and next-generation cDNA sequencing RNA was isolated using Zymo Direct-zol RNA Miniprep kit following manufactures instructions. The RNA quality was checked by Trinean Xpose (Gentbrugge, Belgium) and the Agilent RNA Nano 6000 kit using an Agilent 2100 Bioanalyzer (Agilent Technologies, Böblingen, Germany). Pan-Archaea riboPOOL kit from siTOOLs Biotech was used to remove the rRNA. TruSeq Stranded mRNA Library Prep Kit from Illumina was applied to prepare the cDNA libraries. The cDNAs were sequenced paired end on an Illumina NextSeq 500 system (San Diego, CA, USA) using 74 bp read length mid output. The paired-end cDNA reads were mapped to the Sulfolobus acidocaldarius DSM 639/MW001 genome sequence (accession number CP000077.1) using bowtie2 v2.2.7. with default settings for paired-end read mapping. All mapped sequence data were converted from SAM to BAM format with SAMtools v1.3 and imported to the software ReadXplorer v.2.2.

2024-12-31 | E-MTAB-14293 | biostudies-arrayexpress

Cellular stress response of Sulfolobus acidocaldarius to nutrient limitation

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

Identification of potential interaction partners of the CoxG homologs Saci_1119 and Saci_2031 in Sulfolobus acidocaldarius MW001

Project description:This project aims on the study of glycerol metabolism in the thermoacidophilic crenarchaeal model organism Sulfolobus acidocaldarius, previously regarded as a non-glycerol utilizer. On the one hand, changes in the proteome of the glycerol-adapted strain Sulfolobus acidocaldarius MW00G upon growth with different concentrations of glycerol (10 mM, 20 mM, and 40 mM) as sole carbon and energy source was investigated. On the other hand, potential interaction partners of the two carbon monoxide dehydrogenase subunit G (CoxG) homologs, Saci_1119 and Saci_2031, were identified by overexpression of C-terminally HA-tagged versions of the two CoxG proteins and subsequent co-immunoprecipitation, thereby aiming to elucidate their potential role as membrane anchors for the glycerol-3-phosphate dehydrogenase (G3PDH) from the respective gene cluster.

2025-03-18 | PXD050086 | Pride

Effect of UV irradiation on Sulfolobus acidocaldarius and involvement of the general transcription factor TFB3 in early UV response

Project description:Extremophilic archaea like all organisms experience potentially life-threatening conditions including UV light, which induces severe DNA damage. Since the alternative general transcription factor (GTF) TFB3 has been proposed to play a key role in UV stress response in the thermoacidophilic crenarchaeon Sulfolobus acidocaldarius, we investigated the expression of TFB3 on protein level including in vivo protein-protein interaction studies, tfb3 reporter gene assays and creation of a tfb3 insertion mutant to study early differential gene expression upon UV treatment (after 45 and 90 minutes). Our results allowed differentiating between the TFB3-dependent and TFB3-independent early UV response in S. acidocaldarius. The early TFB3-independent UV response includes the repression of nucleotide biosynthesis and transport, replication and cell cycle progression in order to allow DNA repair. The TFB3-dependent UV response is characterized by the early induction of TFB3, which is a prerequisite for the following TFB3-dependent expression of genes involved in ups pili formation and the Ced DNA importer. Both structures facilitate the transfer of DNA to allow repair via homologous recombination. The fact, that all genes are downregulated in the tfb3 mutant compared to the reference strain, confirms the hypothesis that TFB3 acts as an activator of transcription.

2020-03-20 | GSE112071 | GEO

Transcriptional Response of the thermoacidophilic Archaeon Sulfolobus acidocaldarius to solvent stress exemplified by 1-butanol exposure

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

Response of the thermoacidophilic Archaeon Sulfolobus acidocaldarius to solvent stress

Project description:In this study, we used S. acidocaldarius adapted to two extremes, low pH and high temperature, to study its tolerance and robustness as well as its global cellular response towards organic solvents exemplified by 1-butanol. We were able to identify biofilm formation as primary cellular response to 1-butanol.

2021-03-15 | PXD023858 | Pride

Sulfolobus acidocaldarius

Project description:Extreme thermoacidophilic sulfur-oxidizing archaeon

| PRJNA35727 | ENA

An unusual glycerol-3-phosphate dehydrogenase in Sulfolobus acidocaldarius elucidates the diversity of glycerol metabolism across Archaea.

Project description: Not available

| S-EPMC11962113 | biostudies-literature

Transcriptome analysis of Sulfolobus acidocaldarius DSM 639 under sugar-free and sugar-rich conditions

Project description:Sulfolobus acidocaldarius is an obligate aerobe that grows in hot and acidic environments. S. acidocaldarius have been reported to grow on a variety of organic compounds as carbon and energy sources. However, little is known about systemic elucidation of carbon utilization for biomass formation and energy metabolism in S. acidocaldarius. In this analysis, the effect of glucose on genome-wide transcriptional profiling in S. acidocaldarius DSM 639 was investigated by RNA-Seq technology.

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Sulfolobus acidocaldarius phosphoproteome

Project description:Shotgun phosphoproteome of Sulfolobus acidocaldarius using PAciFIC technique. Briefly, proteins were denatured, alkylated, trypsine digestion, SCX separation Fractionated peptides were analysed on Bruker HCTultra. Data processing and bioinformatics: data from mass spectrometry were then extracted to mgf format using Bruker Data Analysis V4.0 with a MRM script, these were then were searched against the Sulfolobus acidocaldarius database (containing 2223 proteins) downloaded from NCBI in March 2010 using Phenyx V 2.6 (Genebio, Geneva). The searches were performed using parameters as follows: carbamidomethylation of cysteine (fixed modification), oxidation of methionine (variation), and phosphorylation of serine, tyrosine, threonine (variation), trypsin with 2 missed cleavages. Furthermore, other parameters such as parent, MS/MS, tolerances were set at 2.0 and 0.8 Da, respectively, whilst minimum peptide length, z-score, p-value and AC score were set at 5, 5.5, 10-5, and 5.5 respectively.

2014-04-15 | PXD000289 | Pride

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