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Transciptome profile of TrmB and TbsP, Genome-wide binding of TbsP (HVO_2861) in Haloferax volcanii

ABSTRACT: This SuperSeries is composed of the SubSeries listed below.

ORGANISM(S): Haloferax volcanii DS2

PROVIDER: GSE248566 | GEO | 2023/12/01

REPOSITORIES: GEO

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Transciptome profile of TrmB and TbsP in Haloferax volcanii [RNA-seq]

Project description:The hypersaline-adapted archaeon Haloferax volcanii exhibits remarkable plasticity in its morphology, biofilm formation, and motility in response to variations in nutrients and cell density. The transcriptional regulator TrmB maintains the rod shape in the related species Halobacterium salinarum by activating the expression genes involved in gluconeogenesis. Here we investigated the role of TrmB in Hfx. volcanii. The ∆trmB strain rapidly accumulated suppressor mutations in a gene encoding a novel transcriptional regulator, which we name TrmB suppressor, or TbsP. TbsP is required for adhesion to abiotic surfaces and maintains wild-type cell morphology and motility. To better understand the roles of TrmB and TbsP, we conducted expression profiling in ∆trmB, ∆tbsP, ∆trmB∆tbsP in response to glucose availability. TrmB and TbsP jointly regulate the transcription of gapII, fbp, and ppsA.

2023-12-01 | GSE248564 | GEO

Transciptome profile of TrmB and TbsP, Genome-wide binding of TbsP (HVO_2861) in Haloferax volcanii

Project description:Transciptome profile of TrmB and TbsP, Genome-wide binding of TbsP (HVO_2861) in Haloferax volcanii

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Transciptome profile of TrmB and TbsP in Haloferax volcanii [RNA-seq]

Project description:Transciptome profile of TrmB and TbsP in Haloferax volcanii [RNA-seq]

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Genome-wide binding of TbsP (HVO_2861) in Haloferax volcanii [CHIP-seq]

Project description:The hypersaline-adapted archaeon Haloferax volcanii exhibits remarkable plasticity in its morphology, biofilm formation, and motility in response to variations in nutrients and cell density. The transcriptional regulator TrmB maintains the rod shape in the related species Halobacterium salinarum by activating the expression genes involved in gluconeogenesis. Here we investigated the role of TrmB in Hfx. volcanii. The ∆trmB strain rapidly accumulated suppressor mutations in a gene encoding a novel transcriptional regulator, which we name TrmB suppressor, or TbsP. TbsP is required for adhesion to abiotic surfaces and maintains wild-type cell morphology and motility. We identified TbsP binding sites in the presence and absence of glucose to better understand the role of TbsP. TbsP does not bind DNA in response to glucose availability. The sole binding site near a metabolic enzyme-coding gene is upstream of gapII.

2023-12-01 | GSE248565 | GEO

Genome-wide binding (ChIP-Seq) of histone-like protein (HstA) of Haloferax volcanii

Project description:Diverse studies including protemoics, genome-wide binding, and transcriptional profiling of the model halophile Halobacterium salinarum suggest that its putative histone protein acts not as a chromatin protein but a direct and indirect transcriptional regulator. Here, we characterise the putative histone (HstA) of another model halophile (Haloferax volcanii) with ChIP-Seq to understand its genome-wide binding, and compare it with binding patterns seen from histones, nucleoid-associated proteins, and transcription factors of Halobacterium salinarum, other archaea, and eukaryotes. Analysis of this data by visual inspection, start site occupancy profiles, DNA motif searching, and dinucleotide periodicity suggests that the binding mode of halophilic histones shares features with TFs, NAPs, and more typical archaeal/eukaryotic histones.

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Transciptome profile of TrmB in Haloarcula hispanica

Project description:Transcripome profiling (RNA-seq) of TrmB in the halophilic archaeon Haloarcula hispanica in the presence and absense of glucose after 24 hours.

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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

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

Estimation of the Genome-Wide Mutation Rate and Spectrum in the Archaeal Species <i>Haloferax volcanii</i>.

Project description:Organisms adapted to life in extreme habitats (extremophiles) can further our understanding of the mechanisms of genetic stability, particularly replication and repair. Despite the harsh environmental conditions they endure, these extremophiles represent a great deal of the Earth's biodiversity. Here, for the first time in a member of the archaeal domain, we report a genome-wide assay of spontaneous mutations in the halophilic species Haloferax volcanii using a direct and unbiased method: mutation accumulation experiments combined with deep whole-genome sequencing. H. volcanii is a key model organism not only for the study of halophilicity, but also for archaeal biology in general. Our methods measure the genome-wide rate, spectrum, and spatial distribution of spontaneous mutations. The estimated base substitution rate of 3.15 × 10-10 per site per generation, or 0.0012 per genome per generation, is similar to the value found in mesophilic prokaryotes (optimal growth at ∼20-45°). This study contributes to a comprehensive phylogenetic view of how evolutionary forces and molecular mechanisms shape the rate and molecular spectrum of mutations across the tree of life.

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The TroR transcription factor regulates iron homeostasis in the halophilic archaeon Haloferax volcanii

Project description:This SuperSeries is composed of the SubSeries listed below.

2023-11-16 | GSE240622 | GEO