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The TroR transcription factor genome-wide binding analysis in the halophilic archaeon Haloferax volcanii [ChIP-Seq]

ABSTRACT: The TroR transcription factor genome-wide binding analysis in the halophilic archaeon Haloferax volcanii [ChIP-Seq]

PROVIDER: PRJNA1004166 | ENA |

REPOSITORIES: ENA

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			Action	DRS
	SRR25594418.fastq.gz	Fastqsanger.gz
	SRR25594419.fastq.gz	Fastqsanger.gz
	SRR25594420.fastq.gz	Fastqsanger.gz
	SRR25594421.fastq.gz	Fastqsanger.gz
	SRR25594422.fastq.gz	Fastqsanger.gz

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The TroR transcription factor genome-wide binding analysis in the halophilic archaeon Haloferax volcanii [ChIP-Seq]

Project description:Iron is essential for almost all organisms, but can be toxic in excess. Cells use regulatory mechanisms to control the iron uptake, iron utilization and iron release mechanisms to ensure the availability of enough iron to be used for biological processess but minimizing the oxidative stress caused by the oxidation of free molecules of iron. In this paper we show that TroR is a transcription factor from the conserved family of proteins DtxR that directly binds the promoter of a set of genes involved in iron homeostasis meanwhile SirR is not a major regulator of iron homeostasis in the halophilic archaeon Haloferax volcanii.

2023-11-16 | GSE240518 | GEO

The TroR transcription factor regulates iron homeostasis in the halophilic archaeon Haloferax volcanii [RNA-Seq]

Project description:Iron is essential for almost all organisms, but can be toxic in excess. Cells use regulatory mechanisms to control the iron uptake, iron utilization and iron release mechanisms to ensure the availability of enough iron to be used for biological processess but minimizing the oxidative stress caused by the oxidation of free molecules of iron. In this paper we show that TroR is a transcription factor from the conserved family of proteins DtxR that works as the major regulator of iron homeostasis in the halophilic archaeon Haloferax volcanii.

2023-11-16 | GSE240621 | GEO

The Extreme Halophilic Archaeon Haloferax volcanii Reduced Fe(III) to Conserve Energy from Extracellular Electron Transfer

Project description:Iron availability affects oceanic primary productivity and the strength of the biological carbon pump. However, the mechanism of iron solubility in hypersaline environments is poorly understood. In this work, we investigated the extremely halophilic archaeon Haloferax volcanii to reduce ferrihydrite under 25% salinity, aiming to elucidate its energy metabolism associated with extracellular electron transfer (EET). Ferrihydrite reduction by H. volcanii reached a plateau around the eighth day, with an Fe(III) conversion of approximately 41%. The redox-active substances on the cell surface play a central role via EET. Proteomic analysis revealed that the relative abundance of membrane-bound quinoline b-type cytochrome oxidases (A0A841HB82, A0A841HBL7) increased by 73.8% and 120%, respectively, when H. volcanii used ferrihydrite rather than O2 as the terminal electron acceptor. Moreover, H. volcanii was found to secrete riboflavin which can function as an electron shuttle mediating indirect EET. Our findings provide insights into the survival and evolutionary strategies of early life in anaerobic environments on Earth , and the EET capability of H. volcanii highlights its potential applicability in the treatment of pollutants in hypersaline wastewater.

2026-02-08 | PXD074223 |

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

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

| PRJNA1004323 | ENA

The TroR transcription factor regulates iron homeostasis in the halophilic archaeon Haloferax volcanii [RNA-Seq]

Project description:The TroR transcription factor regulates iron homeostasis in the halophilic archaeon Haloferax volcanii [RNA-Seq]

| PRJNA1004320 | ENA

Revealing the small proteome of Haloferax volcanii by ribosome profiling and small-protein optimised mass spectrometry

Project description:We present a combinatorial approach, integrating experimental data from small protein-optimized mass spectrometry (MS) and ribosome profiling (Ribo-seq), to generate a high confidence inventory of small proteins in the model archaeon Haloferax volcanii.

2023-01-18 | GSE208086 | GEO

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

Evolution of genome architecture in Archaea: spontaneous generation of a new chromosome in Haloferax volcanii by homologous recombination

Project description:Eukaryotic genomes typically consist of multiple (linear) chromosomes that are replicated from multiple origins. Several hypothetical scenarios have been proposed to account for the evolution of multi-origin/multi-chromosome genomes, which are encountered in modern eukaryotes and archaea. Here we report an example of the generation of a new chromosome in the halophilic archaeon Haloferax volcanii through one of these scenarios: acquisition of new replication origins and splitting of an ancestral chromosome into two replication-competent chromosomes. The multi-origin main chromosome has split into two genome elements via homologous recombination. The newly generated elements possess all the features of bona fide chromosomes. To our knowledge, the spontaneous generation of a new chromosome in prokaryotes without horizontal gene transfer has not been reported previously.

2018-04-17 | GSE108201 | 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.

2021-10-29 | GSE186415 | GEO

Haloferax volcanii

Project description:Halophilic archaeon

| PRJNA35337 | ENA