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H.volcanii_TTS

ABSTRACT: Transcription termination in the archaeon Haloferax volcanii

PROVIDER: PRJEB30349 | ENA |

REPOSITORIES: ENA

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			Action	DRS
	ERR3011920_1.fastq.gz	Fastqsanger.gz
	ERR3011920_2.fastq.gz	Fastqsanger.gz
	ERR3011881_1.fastq.gz	Fastqsanger.gz
	ERR3011881_2.fastq.gz	Fastqsanger.gz
	ERR3011921.fastq.gz	Fastqsanger.gz

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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

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

Post-transcriptional regulation of redox homeostasis by the small RNA SHOxi in haloarchaea

Project description:Oxidative stress responsive small non-coding RNAs (sRNAs) have been reported in the model archaeon, Haloferax volcanii, but targets and mechanisms of actions have not been elucidated. While haloarchaea are highly resistant to oxidative stress, a comprehensive understanding of the mechanisms regulating this remarkable response is lacking. Here, using a combination of high throughput and reverse molecular genetic approaches we elucidated the functional role of the most up-regulated intergenic sRNA during oxidative stress in H. volcanii, aptly named Small RNA in Haloferax Oxidative Stress (SHOxi). We demonstrated that SHOxi is a functional non-coding RNA that plays gene regulatory roles in the oxidative stress response of an extremophilic archaeon. We found that SHOxi likely regulates redox homeostasis during oxidative stress by the post-transcriptional destabilization of malic enzyme mRNA. The decrease in the NAD+/NADH ratio resulting from the direct RNA-RNA interaction between SHOxi and its trans-target is instrumental in the survival of H. volcanii. The regulatory effects of SHOxi provides evidence that the fine-tuning of metabolic cofactors could be a core strategy to mitigate damage from oxidative stress and confer resistance. This study is the first to establish the regulatory effects of sRNAs on mRNAs during the oxidative stress response in Archaea.

2020-12-08 | GSE158891 | 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

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

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

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Project description:We use MNase-Seq to elucidate primary chromatin architecture in an archaeon without histones, the acido-thermophilic archaeon Thermoplasma acidophilum. Like all members of the Thermoplasmatales, T. acidophilum harbours a HU family protein, HTa, that is highly expressed and protects - like histones but unlike well-characterized bacterial HU proteins – a sizeable fraction of the genome from MNase digestion. Comparing HTa-based chromatin architecture to that of three histone-encoding archaea, Methanothermus fervidus, Haloferax volcanii, and Thermococcus kodakkarensis, we present evidence that HTa is an archaeal histone analog. HTa-protected fragments are GC-rich, display histone-like mono- and dinucleotide patterns around the dyad, exhibit relatively invariant positioning throughout the growth cycle, and show archaeal histone-like oligomerization dynamics. Our results suggest that HTa, a DNA-binding protein of bacterial origin, has converged onto an architectural role filled by histones in other archaea.

2019-03-11 | GSE127727 | GEO

Checking the origin utilisation of Haloferax mediterranei H13 through high-throughput DNA sequencing

Project description:A potential origin that appears to stay dormant in its native host Haloferax volcanii lacking the main active origins becomes activated and competent for replication of the entire chromosome when integrated into the chromosome of the origin-deleted H. mediterranei. Measurement of replication dynamics (marker frequency analysis; MFA) for Haloferax mediterranei H13

2015-07-10 | E-GEOD-70592 | biostudies-arrayexpress

Elucidation of the translation initiation factor interaction network of Haloferax volcanii reveals coupling of transcription and translation in haloarchaea

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

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