Halobacterium salinarum NRC-1
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ABSTRACT:
PROVIDER: PRJNA253194 | ENA |
REPOSITORIES: ENA
Similar Datasets
Project description:RosR is a haloarchaeal-specific transcription factor required for the response to extreme oxidative stress in Halobacterium salinarum NRC-1.
| PRJNA150621 | ENA
Project description:Chemoheterotrophic obligate extreme halophilic archeon
| PRJNA217 | ENA
Project description:Antisense RNAs (asRNAs) are present in diverse organisms and play important roles in gene regulation. In this work, we mapped the primary antisense transcriptome in the halophilic archaeon Halobacterium salinarum NRC-1. By reanalyzing publicly available data, we mapped antisense transcription start sites (aTSSs) and inferred the probable 3' ends of these transcripts. We analyzed the resulting asRNAs according to the size, location, function of genes on the opposite strand, expression levels and conservation. We show that at least 21% of the genes contain asRNAs in H. salinarum. Most of these asRNAs are expressed at low levels. They are located antisense to genes related to distinctive characteristics of H. salinarum, such as bacteriorhodopsin, gas vesicles, transposases and other important biological processes such as translation. We provide evidence to support asRNAs in type II toxin⁻antitoxin systems in archaea. We also analyzed public Ribosome profiling (Ribo-seq) data and found that ~10% of the asRNAs are ribosome-associated non-coding RNAs (rancRNAs), with asRNAs from transposases overrepresented. Using a comparative transcriptomics approach, we found that ~19% of the asRNAs annotated in H. salinarum belong to genes with an ortholog in Haloferax volcanii, in which an aTSS could be identified with positional equivalence. This shows that most asRNAs are not conserved between these halophilic archaea.
| S-EPMC6523106 | biostudies-literature
Project description:Previous work has shown that the hypersaline-adapted archaeon, Halobacterium salinarum NRC-1, is highly resistant to oxidative stress caused by exposure to hydrogen peroxide, UV and gamma radiation. Genome-wide dynamics alteration of gene the GRN has been implicated in such resistance. However, the molecular function of transcription regulatory proteins involved in this response remains unknown. Here we have leveraged several existing GRN and systems biology datasets for H. salinarum to identify and characterize a novel winged helix-turn-helix transcription factor, VNG0258H, as a regulator required for reactive oxygen species resistance in this organism. This protein appears to be unique to the haloarchaea at the primary sequence level. Quantitative growth assays in a deletion mutant strain implicate VNG0258H in extreme oxidative stress resistance. According to time course gene expression analyses, this transcription factor is required for the appropriate dynamic response of nearly 300 genes to reactive oxygen species damage from paraquat and hydrogen peroxide. These genes are predicted to function in repair of oxidative damage to proteins and DNA. in vivo DNA binding assays (ChIP-qPCR) demonstrate that VNG0258H binds DNA to mediate gene regulation. Together these results suggest that VNG0258H is a novel archaeal transcription regulatory protein that regulates gene expression to enable adaptation to the extremely oxidative, hypersaline niche of H. salinarum. We have therefore renamed VNG0258H as RosR, for reactive oxygen species regulator. Data in this archive are linked to the publication Sharma KS, Gillum NA, Schmid AK 2012
2012-08-13 | GSE33980 | GEO
Project description:Halobacterium salinarum NRC-1 was grown in CM media, at 37oC in a waterbath with agitation of 125 rpm under constant light. Analysis of transcriptional changes during growth, in addition to mapping of transcriptome structure under the same conditions, provided interesting insights about regulatory logic within prokaryotic coding regions.
2009-06-25 | GSE12977 | GEO
Project description:Gene regulatory networks play an important role in coordinating biochemical fluxes through diverse metabolic pathways. The modulation of enzyme levels enables efficient utilization of limited resources as organisms dynamically acclimate to nutritional fluctuations in their environment. Here we have identified and characterized a novel nutrient-responsive transcription factor from the halophilic archaea, AgmR. Like TrmB, its thermophilic archaeal homolog, AgmR regulates glycolytic and gluconeogenic pathways in response to sugar availability. However, using high throughput genome-scale experiments, we find that AgmR directly governs the transcription of nearly 100 additional genes encoding enzymes in diverse metabolic pathways. Genome-scale in vivo binding site location data reveals that >60% of these are direct targets. Integration of these systems-scale datasets with metabolic reconstruction models suggests that AgmR, a sequence-specific bacterial-like regulator, interacts with the general transcription factor machinery to coordinate nitrogen and carbon metabolism with the de novo synthesis of cognate cofactors and reducing equivalents, achieving system-wide redox and energy balance.
2009-09-08 | GSE13498 | GEO
Project description:Previous work has shown that the hypersaline-adapted archaeon, Halobacterium salinarum NRC-1, is highly resistant to oxidative stress caused by exposure to hydrogen peroxide, UV and gamma radiation. Genome-wide dynamics alteration of gene the GRN has been implicated in such resistance. However, the molecular function of transcription regulatory proteins involved in this response remains unknown. Here we have leveraged several existing GRN and systems biology datasets for H. salinarum to identify and characterize a novel winged helix-turn-helix transcription factor, VNG0258H, as a regulator required for reactive oxygen species resistance in this organism. This protein appears to be unique to the haloarchaea at the primary sequence level. Quantitative growth assays in a deletion mutant strain implicate VNG0258H in extreme oxidative stress resistance. According to time course gene expression analyses, this transcription factor is required for the appropriate dynamic response of nearly 300 genes to reactive oxygen species damage from paraquat and hydrogen peroxide. These genes are predicted to function in repair of oxidative damage to proteins and DNA. in vivo DNA binding assays (ChIP-qPCR) demonstrate that VNG0258H binds DNA to mediate gene regulation. Together these results suggest that VNG0258H is a novel archaeal transcription regulatory protein that regulates gene expression to enable adaptation to the extremely oxidative, hypersaline niche of H. salinarum. We have therefore renamed VNG0258H as RosR, for reactive oxygen species regulator. Data in this archive are linked to the publication Sharma KS, Gillum NA, Schmid AK 2012 The M-NM-^Tura3 and M-NM-^TrosR strains were grown to mid-logarithmic phase (OD600 ~ 0.5) in CM supplemented with uracil. For the H2O2 time courses, 4 ML culture aliquots were removed for RNA extraction at three time points prior to the addition of H2O2 (-40 min, -20 min, 0min) and five time points following H2O2 addition (10 min, 20 min, 40 min, 60 min, 80 min). Paraquat time courses were prepared similarly with the exception that additional time points were taken at 2h, 8h, and 24 h after the addition of paraquat. RNA from two biological replicate time courses were prepared, along with a dye filip.
2012-08-12 | E-GEOD-33980 | biostudies-arrayexpress
Project description:Evolution of Context Dependent Regulation by Expansion of Feast/Famine Regulatory Proteins [expression]
| PRJNA262850 | ENA
Project description:Evolution of Context Dependent Regulation by Expansion of Feast/Famine Regulatory Proteins [ChIP-chip]
| PRJNA263042 | ENA
Project description:Experimentally mapped transcriptome structure of H. salinarum NRC-1 by hybridizing total RNA (including RNA species <200 nt) to genome-wide high-density tiling arrays (60 mer probes with 40 nt overlap between contiguous probes). H. salinarum NRC-1 presents a number of interesting switches in metabolism during growth due to complex changes in EFs including pH, oxygen, nutrition, etc. While most single perturbations (radiation, oxygen, metals, etc.) affect the expression of only ~10% of all genes (Baliga et al, 2004; Kauret al , 2006; Whitehead et al, 2006), the changes during growth resulted in differential regulation of a significantly higher proportion of genes (~63%, 1,518 genes). These conditions enabled the investigation of a wider transcriptional landscape, which includes not only modulation of transcript levels, but also extensive changes in transcriptome structure. We observed altered transcription start sites (TSSs), transcription termination site (TTSs), operon organizations and differential regulation of putative ncRNAs. By integrating hybridization signals with dynamic growth-related changes, we estimated the probability that each tiling array probe was complementary to a transcribed region, mapped locations of putative transcript boundaries and identified 1,574 TSSs and 1,952 TTSs for most genes with some transcriptional variation. In sum, TSSs were assigned to 64% (1,156 singletons and 544 genes in 203 operons) of all annotated genes and TTSs were assigned to 1,114 genes and 202 operons. We were also able to identify 5' and 3' UTRs and revise start sites for 61 genes and 12 operons.
2009-06-25 | GSE12923 | GEO