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Genome-wide gene expression Haloferax volcanii under oxidative stress

ABSTRACT: Genome-wide gene expression Haloferax volcanii under oxidative stress

PROVIDER: PRJNA842435 | ENA |

REPOSITORIES: ENA

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Genome-wide gene expression Haloferax volcanii under oxidative stress

Project description:The goals of this study are to compare NGS-derived transcriptome profiling (RNA-seq) of H. volcanii upon treatment of NaOCl.

2022-05-25 | GSE204840 | GEO

Transcriptional Landscape and Regulatory Roles of Small Noncoding RNAs in the Oxidative Stress Response of the Haloarchaeon Haloferax volcanii

Project description:We demonstrate here the transcriptional landscape and functional roles of sRNAs specifically in the regulation of the oxidative stress response of the model haloarchaeon Haloferax volcanii. We sequenced 5 biological replicates of H. volcanii strain H53 under no challenge and oxidative stress (H2O2) conditions at mid-exponential phase (OD 0.4). Thousands of sRNAs, both intergenic and antisense, were discovered using strand-specific sRNA-seq, comprising around 30% of the transcriptome during non-challenged and oxidative stress conditions. Antisense sRNAs were found to overlap both 5’ and 3’ UTRs of mRNAs revealing a hybrid system between Eukarya (3’ UTR) and Bacteria (5’ UTR) sRNA-silencing systems, as well as targeting the coding sequence (CDS) of mRNAs, a unique system to Archaea. We identified hundreds of differentially expressed sRNAs in response to hydrogen peroxide induced oxidative stress in H. volcanii. A majority of these sRNAs are lowly expressed compared to mRNAs. The sRNAs could be classified in two populations based on expression patterns: those that are up-regulated and those that are down-regulated during oxidative stress. Targets of antisense sRNAs decreased in expression when sRNAs were up-regulated indicating that sRNAs are likely playing a negative regulatory role on mRNA targets at the transcript level. Target enrichment of sRNAs included mRNAs involved in transposons, chemotaxis signaling, peptidase activity, transcription factors, and secondary metabolite regulation.

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Project description:Structural and functional adaptation of Haloferax volcanii TFEα/β

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Structural and functional adaptation of Haloferax volcanii TFEα/β

Project description:Purpose: The Haloferax volcanii ∆tfeB strain provided a unique opportunity to study a putative role of TFEβ in the regulation of gene expression. Results: The deletion of the tfeB gene in H. volcanii results in the aberrant expression of approximately one third of all genes, consistent with its function as a basal transcription initiation factor. Interestingly, tfeB deletion particularly affects foreign genes including a prophage region. Conclusions: Our results confirm the dual function of TFE as basal factor and regulator of transcription

2017-12-08 | GSE101134 | GEO

TrmB-like family transcription factor OxsR regulates the oxidative stress response in Haloferax volcanii

Project description:Haloarchaea tolerate high levels of reactive species that are naturally present in hypersaline environments. Hundreds of sRNAs, transcripts, and proteins are found altered in abundance when haloarchaea are exposed to reactive species, yet the regulators that control these responses are not well characterized. Here we report the function of Haloferax volcanii OxsR (redox stress responsive regulator, HVO_2970), a standalone winged-helix DNA binding domain protein of the TrmB-like family. Here we demonstrate that OxsR is important for growth in the presence of hypochlorite and binds specific regions of genomic DNA during hypochlorite stress by ChIP-seq analysis. The OxsR-bound intergenic regions were located nearby operons encoding oxidative stress functions, including the biosynthesis of low molecular weight thiols and thiol relay systems. Further analysis by qRT-PCR revealed that OxsR functions during oxidative stress largely as a transcriptional activator, and occasionally as a repressor. The conserved cysteine residue (C24) of OxsR and a CG-rich binding motif upstream of BRE/TATA box promoter elements were found important in the transcriptional activation of select operons during hypochlorite stress. 3D-modeling of OxsR revealed C24 to be located at a homodimer interface formed by antiparallel α1 helices, suggesting that C24 forms an intersubunit disulfide bond in the presence of oxidant that stabilizes the homodimer. The phylogenetic distribution of OxsR homologs with the conserved cysteine suggests this type of redox signaling mechanism is widespread in Archaea.

2022-02-18 | GSE196894 | GEO

Transcription analysis for the growth of Haloferax volcanii on L-alanine and ammonium chloride

Project description:Identification of global gene expression profiling when Haloferax volcanii H26 strain is grown in minimal medium supplemented with two nitrogen sources, 10 mM L-alanine and 10 mM ammonium chloride.

2019-08-21 | GSE130934 | GEO

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