Halobacterium salinarum NRC-1
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ABSTRACT:
OTHER RELATED OMICS DATASETS IN: PRD000472
REPOSITORIES: ENA
Similar Datasets
Project description:Chemoheterotrophic obligate extreme halophilic archeon
| PRJNA106 | ENA
Project description:Chemoheterotrophic obligate extreme halophilic archeon
| PRJNA105 | 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:Halobacterium salinarum is an extreme halophilic archaeon adapted to total salinities upwards of 4 M. Here we studied gene expression in H. salinarum grown in ten ion composition media that vary in two major aspects of ion composition: [NaCl] and Mg:K ratio.
2013-12-21 | GSE53544 | GEO
Project description:A regulatory hierarchy controls the dynamic transcriptional response to extreme oxidative stress in archaea.
| PRJNA253194 | ENA
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:To investigate the contribution of ribonucleases to post-transcriptional regulation of mRNA levels, we examined the fitness consequences and gene expression changes of ribonuclease mutants in the extreme halophilic archaeon Halobacterium salinarum NRC-1. H. salinarum NRC-1 is known to use a large repertoire of environment-specific transcriptional regulatory programs, which may be complemented by post-transcriptional regulatory mechanisms. Homology searches identified putative RNase genes in H. salinarum NRC-1 that include likely orthologs for RNases found in prokaryotic and eukaryotic lineages. The VNG2099C protein sequence is significantly similar (e = 2 x 10^-34) to the sequence of the rat liver perchloric acid-soluble protein (L-PSP), which has been shown to have endoribonuclease activity in vitro (Morishita et al 1999). The VNG2099C protein, like the archaeal Sulfolobus tokodaii YjgF/L-PSP protein for which a crystal structure has been solved (Miyakawa et al 2006), shares conservation of residues proposed to constitute the active site of the rat protein. The purpose of this gene expression study was to investigate the role of the putative endoribonuclease VNG2099C on gene regulation.
2014-03-03 | GSE45988 | 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:Data-Independent Acquisition (DIA) is a mass spectrometry-based method to reliably identify and reproducibly quantify large fractions of a target proteome. The peptide-centric data analysis strategy employed in DIA requires a priori generated spectral assay libraries. Such assay libraries allow to extract quantitative data in a targeted approach and have been generated for human, mouse, zebrafish, E. coli and few other organisms. However, a spectral assay library for the extreme halophilic archaeon Halobacterium salinarum NRC-1, a model organism that contributed to several notable discoveries, is not publicly available yet. Here, we report a comprehensive spectral assay library to measure 2,563 of 2,646 annotated H. salinarum NRC-1 proteins. We demonstrate the utility of this library by measuring global protein abundances over time under standard growth conditions. The H. salinarum NRC-1 library includes 21,074 distinct peptides representing 97% of the predicted proteome and provides a new, valuable resource to confidently measure and quantify any protein of this archaeon.
2023-09-21 | PXD042770 | Pride