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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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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

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

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

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

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

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

| PRJEB43039 | ENA

RNA-seq analysis of Entamoeba histolytica glycerol 3-phosphate dehydrogenase (G3PDH) and glycerol kinase (EhGK) gene silencing strain

Project description:Amebiasis is caused by the protozoan parasite Entamoeba histolytica. Treatment options other than metronidazole and its derivatives are few, and their low efficacy against asymptomatic cyst carriers, and experimental evidence of resistance in vitro justify the discovery/repurposing campaign for new drugs against amebiasis. To better understand the role of glycerol metabolism in this parasite, we focused on characterizing two important enzymes, glycerol kinase (GK) and glycerol 3-phosphate dehydrogenase (G3PDH). Recombinant GK was biochemically characterized in detail, while G3PDH was not due to failure of protein expression and purification. GK revealed novel characteristics and unprecedented kinetic properties in reverse reaction. Gene silencing revealed that GK is essential for optimum growth, whereas G3PDH is not. Gene silencing of G3PDH caused upregulated GK expression, while that of GK resulted in upregulation of antioxidant enzymes as shown by RNA-seq analysis. Although the precise molecular link between GK and the upregulation of antioxidant enzymes was not demonstrated, the observed increase in antioxidant enzyme expression upon GK gene silencing suggests a potential connection between GK and the cellular response to oxidative stress. Together, these results provide the first direct evidence of the biological importance and coordinated regulation of the glycerol metabolic pathways for proliferation and antioxidative defense in E. histolytica, justifying the exploitation of these enzymes as future drug targets.

2023-08-14 | GSE240436 | GEO

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.

2020-11-15 | GSE107083 | GEO

Alicyclobacillus acidocaldarius subsp. acidocaldarius HSU9

Project description:Alicyclobacillus acidocaldarius subsp. acidocaldarius HSU9 Genome sequencing

| PRJNA168064 | ENA

Aspergillus nidulans gfdB, encoding the hyperosmotic stress protein glycerol-3-phosphate dehydrogenase, disturbs osmoadaptation in Aspergillus wentii

Project description:The genome of the osmophilic Aspergillus wentii, unlike that of the osmotolerant Aspergillus nidulans, contains only the gfdA but not the gfdB glycerol 3-phosphate dehydrogenase gene. Here, we studied transcriptomic changes of A. nidulans (reference strain and DgfdB gene deletion mutant) and A. wentii (reference strain and An-gfdB expressing mutant) elicited by high osmolarity. A. nidulans showed canonic hyperosmotic stress response characterized by upregulation of trehalose and glycerol metabolism genes (including gfdB) as well as genes of the high-osmolarity glycerol (HOG) map kinase pathway. Deletion of gfdB caused only negligible alterations in the transcriptome suggesting that the glycerol metabolism was flexible enough to compensate for the missing GfdB activity in this species. A. wentii responded differently to increased osmolarity than A. nidulans: E.g.; bulk upregulation of glycerol and trehalose metabolism genes as well as HOG pathway genes were not detected. Expression of An-gfdB in A. wentii did not abolish osmophilia, but it reduced growth and caused much bigger alterations in the transcriptome than the missing gfdB gene did in A. nidulans. Flexible glycerol metabolism and hence two differently regulated gfd genes may be more beneficial for osmotolerant (living under changing osmolarity) than for osmophilic (living under constantly high osmolarity) species.

2024-02-28 | GSE255841 | GEO

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