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Halobacterium NRC-1 in response to oxic/anoxic transitions (initial and verification experiments)

ABSTRACT: This SuperSeries is composed of the SubSeries listed below.

ORGANISM(S): Halobacterium salinarum NRC-1

PROVIDER: GSE5929 | GEO | 2007/07/31

SECONDARY ACCESSION(S): PRJNA97377

REPOSITORIES: GEO

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RNA expression data from Halobacterium NRC-1 in response to oxic/anoxic transitions, verification experiment

Project description:In order to ensure the reproducibility of the transcriptional response of Halobacterium NRC-1 to oxic/anoxic transitions, we repeated global mRNA measurements for the oxygen time series data in GSE5924, except that cultures were equilibrated to high oxygen for 12 hours prior to the start of the experiment rather than low oxygen. The results of these data suggest that there is good (~60%) reproducibility between datasets, and that Halobacterium responds robustly to oxic/anoxic transitions. Keywords: time series

2007-07-31 | GSE5925 | GEO

RNA expression data from Halobacterium NRC-1 in response to oxic/anoxic transitions, initial experiment

Project description:To gain a comprehensive systems-level understanding of cellular phenotypes, it is critical to characterize the relationship between the dynamic transcriptome and proteome during environmental perturbations. Previous comparisons have shown a lack of correlation between mRNA and protein level measurements suggesting a predominant role for post-transcriptional regulation in mediating cellular environmental responses. To investigate the extent of post-transcriptional regulation, we have analyzed transcriptome and proteome level changes over a 13-hour 28-point time course during transitions between oxic and anoxic physiologies of Halobacterium. Integrated computational analyses of these data show that temporally shifting mRNA and protein profiles relative to one another significantly increases the mRNA/protein correlation. Although time lags for unrelated genes vary widely, we observe similar temporal lags between the transcription and translation of functionally related genes. In contrast, no significant temporal separation was observed within the transcript profiles. Taken together, these data suggest that while there is indeed a direct correlation between many corresponding changes at mRNA and protein levels, translational delay may be the predominant mechanism for the temporal regulation of protein abundance during physiological oxic/anoxic transitions in Halobacterium. The approach and algorithms delineated in this study provide a framework for incorporating the temporal dimension of information processing across many different layers of gene regulation. Keywords: time course

2007-07-31 | GSE5924 | GEO

Halobacterium NRC-1 in response to oxic/anoxic transitions (initial and verification experiments)

Project description:Halobacterium NRC-1 in response to oxic/anoxic transitions (initial and verification experiments)

| PRJNA97377 | ENA

Diurnally synchronized transitions between oxic and anoxic physiologies in an archaeon

Project description:This SuperSeries is composed of the SubSeries listed below.

2009-04-14 | GSE15282 | GEO

Metatranscriptomic analyses of plankton communities inhabiting surface and subpycnocline waters of the Chesapeake Bay during oxic-anoxic-oxic transitions.

Project description: Not available

| S-EPMC3910987 | biostudies-literature

Genome sequence of Halobacterium species NRC-1.

Project description: Not available

| S-EPMC17314 | biostudies-literature

Diurnally synchronized transitions between oxic and anoxic physiologies in an archaeon

Project description:This SuperSeries is composed of the following subset Series: GSE15272: Diurnally synchronized transitions between oxic and anoxic physiologies in an archaeon, experiment "A" GSE15273: Diurnally synchronized transitions between oxic and anoxic physiologies in an archaeon, experiment "B" GSE15274: Diurnally synchronized transitions between oxic and anoxic physiologies in an archaeon, experiment "Control-1" GSE15275: Diurnally synchronized transitions between oxic and anoxic physiologies in an archaeon, experiment "C" GSE15276: Diurnally synchronized transitions between oxic and anoxic physiologies in an archaeon, experiment "Control-2" Refer to individual Series

2009-04-14 | E-GEOD-15282 | biostudies-arrayexpress

The Primary Antisense Transcriptome of Halobacterium salinarum NRC-1.

Project description: Not available

| S-EPMC6523106 | biostudies-literature

Diurnally synchronized transitions between oxic and anoxic physiologies in an archaeon, experiment "B"

Project description:By sensing changes in one or few environmental factors biological systems can anticipate future changes in multiple factors over a wide range of time scales (daily to seasonal). This anticipatory behavior is important to the fitness of diverse species, and in context of the diurnal cycle it is overall typical of eukaryotes and some photoautotrophic bacteria but is yet to be observed in archaea. Here, we report the first observation of light-dark (LD)-entrained diurnal oscillatory transcription in up to 12% of all genes of a halophilic archaeon Halobacterium salinarum NRC-1. Significantly, the diurnally entrained transcription was observed under constant darkness after removal of the LD stimulus (free-running rhythms). The memory of diurnal entrainment was also associated with the synchronization of oxic and anoxic physiologies to the LD cycle. Our results suggest that under nutrient limited conditions halophilic archaea take advantage of the causal influence of sunlight (via temperature) on O2 diffusivity in a closed hypersaline environment to streamline their physiology and operate oxically during nighttime and anoxically during daytime.

2009-04-15 | GSE15273 | GEO

Diurnally synchronized transitions between oxic and anoxic physiologies in an archaeon, experiment "C"

2009-04-15 | GSE15275 | GEO

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