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RNA expression data from Halobacterium NRC-1 in varied extracellular salinity conditions

ABSTRACT: 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.

ORGANISM(S): Halobacterium salinarum NRC-1

PROVIDER: GSE53544 | GEO | 2013/12/21

SECONDARY ACCESSION(S): PRJNA232350

REPOSITORIES: GEO

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RNA expression data from Halobacterium NRC-1 in varied extracellular salinity conditions

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. Samples were taken from the M-NM-^Tura3 parental strain cells at mid-log phase (OD600 = 0.4-0.5) during growth in ten different media. RNA from growth in each media was compared with a standard RNA reference, extracted from H. salinarum NRC-1 grown in batch culture in the standard growth media to OD = 0.471. Two biological replicates were performed for each media, with the exception of one replicate only for M12.

2013-12-21 | E-GEOD-53544 | biostudies-arrayexpress

A comprehensive spectral assay library to quantify the Halobacterium salinarum NRC-1 proteome by DIA/SWATH-MS

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

DIA/SWATH-MS analysis of Halobacterium salinarum NRC-1 collected at four time points of batch culture growth

2023-09-21 | PXD042774 | Pride

Measurement of mRNA decay in exponentially growing cultures of the extremely halophilic euryarchaeon Halobacterium salinarum NRC-1 after blocking transcription with actinomycin D

Project description:mRNA half-lives in exponentially growing cultures of the extremely halophilic euryarchaeon Halobacterium salinarum NRC-1

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H. salinarum NRC-1 vs VNG2099C knockout

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

Halobacterium salinarum

Project description:Halophilic archaeon

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H. salinarum NRC-1 vs VNG2099C knockout

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 toM-BM- investigate the role of the putative endoribonuclease VNG2099C on gene regulation. The relative changes in transcript levels were determined for wild type (Dura3) and the VNG2099C knockout.

2014-03-03 | E-GEOD-45988 | biostudies-arrayexpress

How to cope with heavy metal ions: Insights into cellular and molecular stress response in Halobacterium salinarum R1 planktonic cells and biofilms

Project description:Halobacterium salinarum R1 is an extremely halophilic archaeon capable of adhesion and biofilm formation. We have recently shown that living in biofilms facilitates higher cell survival under heavy metal ion stress in this species, while specific rearrangements of the biofilm architecture were observed upon Ni2+ and Cu2+ exposition, respectively. In this study, quantitative analyses were performed by SWATH-LC-MS/MS to determine the respective proteomes under the influences of Ni2+ and Cu2+ in planktonic and biofilm cells. Quantitative data for 1180 proteins were gained, corresponding to 46% of the predicted proteome. In planktonic cells, 234 proteins showed significant abundance changes after metal ion treatment, of which 47% occurred combined in Cu2+ and Ni2+ treated samples. Regarding biofilms, significant changes were detected for 52 proteins. Only three proteins changed under both conditions, suggesting metal-specific stress responses in biofilms.

2020-05-27 | PXD015192 | Pride

Halobacterium NRC-1 VNG1451C deletion mutant growth in defined medium with and without glucose

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, VNG1451C. In this experiment we used whole-genome microarray analysis in the VNG1451C deletion mutant vs. H. salinarum NRC-1 ura3 parent strain in defined medium during growth with and without glucose to show that the expression of many metabolic genes is perturbed in the VNG1451C deletion mutant in response to this sugar.

2009-09-08 | GSE13529 | GEO

Halobacterium NRC-1 ura3 parent strain and VNG1451C deletion mutant in response to growth in rich medium

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, VNG1451C. In this experiment we used whole-genome microarray analysis in the VNG1451C deletion mutant vs. H. salinarum NRC-1 ura3 parent strain in rich medium during growth to show that the expression of many metabolic genes is perturbed in the VNG1451C deletion mutant.

2009-09-08 | GSE13531 | GEO

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