Haloferax volcanii
Ontology highlight
ABSTRACT:
PROVIDER: PRJNA35337 | ENA |
REPOSITORIES: ENA
Similar Datasets
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
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
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
Project description:Halophilic organism isolated from the Dead Sea
| PRJNA12524 | ENA
Project description:Oxidative stress adaptation strategies are important to cell function and are linked to cardiac, neurodegenerative disease and cancer. Representatives of the domain Archaea are used as model organisms based on their extreme tolerance to oxidants and close evolutionary relationship with eukaryotes. Study of the halophilic archaeon Haloferax volcanii reveals lysine acetylation to be associated with oxidative stress responses. The strong oxidant hypochlorite: i) stimulates an increase in lysine acetyltransferase HvPat2 to HvPat1 abundance ratios and ii) selects for lysine deacetylase sir2 mutants. Here we report the dynamic occupancy of the lysine acetylome of glycerol-grown H. volcanii as it shifts in profile in response to hypochlorite. These findings are revealed by the: 1) quantitative multiplex LC-MS/MS analysis of the SILAC-compatible parent and Δsir2 mutant strains and 2) label free LC-MS/MS analysis of H26 ‘wild type’ cells. The results show that lysine acetylation is associated with key biological processes including DNA topology, central metabolism, cobalamin biosynthesis and translation. Lysine acetylation targets are found conserved across species. Moreover, lysine residues modified by acetylation and ubiquitin-like sampylation are identified suggesting post-translational modification (PTM) crosstalk. Overall, the results of this study expand the current knowledge of lysine acetylation in Archaea, with the long-term goal to provide a balanced evolutionary perspective of PTM systems in living organisms.
2023-07-20 | PXD041799 | Pride
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
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
Project description:Translation is an important step in gene expression. Initiation of translation is rate-limiting, and it is 13 phylogenetically more diverse than elongation or termination. Bacteria contain only three initiation 14 factors. In stark contrast, eukaryotes contain more than 10 (subunits of) initiation factors (eIFs). The 15 genomes of archaea contain many genes that are annotated to encode archaeal homologs of 16 eukaryotic initiation factors (aIFs). However, experimental characterization of aIFs is scarce and 17 mostly restricted to very few species. To broaden the view, the protein-protein interaction network of 18 aIFs in the halophilic archaeon Haloferax volcanii has been characterized. To this end, tagged 19 versions of 14 aIFs were overproduced, affinity isolated, and the co-isolated binding partners were 20 identified by peptide mass fingerprinting.
2021-09-29 | PXD028666 | Pride
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
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