Halobacterium salinarum NRC-1 conditional ChIP-chip for transcription initiation factor IIB 4 (TFBd)
Ontology highlight
ABSTRACT:
ORGANISM(S): Halobacterium sp. NRC-1
SUBMITTER: Min Pan
PROVIDER: E-GEOD-13108 | biostudies-arrayexpress |
REPOSITORIES: biostudies-arrayexpress
Publications
Prevalence of transcription promoters within archaeal operons and coding sequences.
Koide Tie T Reiss David J DJ Bare J Christopher JC Pang Wyming Lee WL Facciotti Marc T MT Schmid Amy K AK Pan Min M Marzolf Bruz B Van Phu T PT Lo Fang-Yin FY Pratap Abhishek A Deutsch Eric W EW Peterson Amelia A Martin Dan D Baliga Nitin S NS
Molecular systems biology 20090616
Despite the knowledge of complex prokaryotic-transcription mechanisms, generalized rules, such as the simplified organization of genes into operons with well-defined promoters and terminators, have had a significant role in systems analysis of regulatory logic in both bacteria and archaea. Here, we have investigated the prevalence of alternate regulatory mechanisms through genome-wide characterization of transcript structures of approximately 64% of all genes, including putative non-coding RNAs ...[more]
Similar Datasets
Project description:This SuperSeries is composed of the following subset Series: GSE12923: Halobacterium salinarum NRC-1 growth curve, tiling arrays. GSE12977: Halobacterium salinarum NRC-1 growth curve GSE13108: Halobacterium salinarum NRC-1 conditional ChIP-chip for transcription initiation factor IIB 4 (TFBd) GSE7045: ChIP-Chip of General Transcription factors in Halobacterium NRC-1 GSE15786: Halobacterium sp. NRC-1 ChIP-chip for TFBa, TFBd and TFBf, high resolution array GSE15788: Halobacterium salinarum NRC-1 total RNA hybridization of TFBd overexpression versus Reference sample Despite knowledge of complex prokaryotic transcription mechanisms, generalized rules, such as the simplified organization of genes into operons with well-defined promoters and terminators, have played a significant role in systems analysis of regulatory logic in both bacteria and archaea. Here, we have investigated the prevalence of alternate regulatory mechanisms through genome-wide characterization of transcript structures of ~64% of all genes including putative non-coding RNAs in Halobacterium salinarum NRC-1. Our integrative analysis of transcriptome dynamics and protein-DNA interaction datasets revealed widespread environment-dependent modulation of operon architectures, transcription initiation and termination inside coding sequences, and extensive overlap in 3' ends of transcripts for many convergently transcribed genes. A significant fraction of these alternate transcriptional events correlate to binding locations of 11 transcription factors and regulators (TFs) inside operons and annotated genes - events usually considered spurious or non-functional. With experimental validation, we illustrate the prevalence of overlapping genomic signals in archaeal transcription, casting doubt on the general perception of rigid boundaries between coding sequences and regulatory elements Refer to individual Series
2010-05-17 | E-GEOD-13150 | biostudies-arrayexpress
Project description:Oxidative stress (OS) results from genetic defects or stressful environmental challenges that cause unchecked production of reactive oxygen species (ROS). OS has been implicated in many diseases due to its wide ranging damage to nucleic acids, proteins and lipids. Using Halobacterium salinarum NRC-1, an extremophile that thrives under conditions of excessive OS, we have constructed a systems model for oxidative stress response (OSR) by integrating transcriptional changes induced by treatments with H2O2 and paraquat, functional associations inferred through comparative genomics, and de novo discovered cis-regulatory motifs. Together with phenotypic analysis of mutant strains this has revealed a multi-tiered OS management program to transcriptionally coordinate three peroxidase/catalase enzymes, two superoxide dismutases, production of rhodopsins, carotenoids, and gas vesicles, metal trafficking, and various other aspects of metabolism. Remarkably, a significant fraction of this OSR was accurately recapitulated by a model that was previously constructed from cellular responses to diverse environmental perturbations –this constitutes the general stress response component. Notwithstanding this observation, comparison of the two models has identified the coordination of frontline defense and repair systems by regulatory mechanisms that are triggered uniquely by severe OS and not by other environmental stressors, including sub-inhibitory levels of redox-active metals, extreme changes in oxygen tension, and a sub-lethal dose of g rays. Mid-log phase cultures of H. salinarum NRC-1 (2 biological replicates) grown in flasks were treated with either sub-lethal concentrations of 25mM H2O2 or 4mM PQ and incubated with shaking for up to 240 min. For each treatment, two time courses were run to determine the transcriptional responses to (1) constant stress and (2) recovery of H. salinarum NRC-1 to H2O2 and PQ. During constant stress, culture aliquots (~4ml) were collected over a time course (-1, 5, 10, 20, 40, 80 and 160 minutes), centrifuged (16000g, 90 seconds) and flash frozen. For recovery, cells were first treated for 2-hours with either 25 mM H2O2 or 4mM PQ, recovered by centrifugation, washed and re-suspended in CM. Cultures were returned to the incubator with shaking and samples were taken at 0, 10, 20, 30, 40, 50, 60, 120, and 240 minutes and processed as described previously. Analysis of temporal transcriptional changes (-1, 0, 5, 10, 20, 40, 80, 160 and 320m) to sub-inhibitory concentrations of PQ (0.25mM) was also characterized. Total RNA was prepared and labeled with Alexa547 and Alexa647 dyes. Intensities were normalized between the Alexa 546 and Alexa 647 channels by scaling all intensities in one channel such that the 75th percentile in each channel was made equal.
2010-05-26 | E-GEOD-17515 | biostudies-arrayexpress
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. This publication consists of five experiments, known as A, B, C, Control-1, and Control-2. A,B, and C are entrained as described in the publication, and Control-1 and Control-2 were not entrained.
2010-06-19 | E-GEOD-15272 | biostudies-arrayexpress
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. This publication consists of five experiments, known as A, B, C, Control-1, and Control-2. A,B, and C are entrained as described in the publication, and Control-1 and Control-2 were not entrained.
2010-06-19 | E-GEOD-15274 | biostudies-arrayexpress
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. This publication consists of five experiments, known as A, B, C, Control-1, and Control-2. A,B, and C are entrained as described in the publication, and Control-1 and Control-2 were not entrained.
2010-06-19 | E-GEOD-15273 | biostudies-arrayexpress
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. This publication consists of five experiments, known as A, B, C, Control-1, and Control-2. A,B, and C are entrained as described in the publication, and Control-1 and Control-2 were not entrained.
2010-10-08 | E-GEOD-15275 | biostudies-arrayexpress
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. This publication consists of five experiments, known as A, B, C, Control-1, and Control-2. A,B, and C are entrained as described in the publication, and Control-1 and Control-2 were not entrained.
2010-06-19 | E-GEOD-15276 | biostudies-arrayexpress
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
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. Samples were collected at different cell densities, from OD ~0.2 to OD ~5.0. 2 biological replicates were conducted. For each sample, a dye-swap experiment was performed.
2010-05-17 | E-GEOD-12977 | biostudies-arrayexpress
Project description:We report detailed characterization of physiological changes encoded by 63% of all genes within the archaeon Halobacterium salinarum subsp. NRC-1 during routine laboratory growth. While the majority of these changes occur during the transition from rapid exponential growth to the stationary phase, we were also able to detect transient changes in gene expression. This demonstrated the presence of several additional albeit subtle physiological states that exist beyond what might be anticipated from a direct interpretation of the growth profile. Changes in the abundance of several key intracellular metabolites over the growth curve corroborated observations of changes in gene expression of enzymes that catalyze their synthesis. Next, we investigated the roles of general transcription factors (GTFs) in mediating these global growth-associated gene expression changes. This revealed numerous phenotypic perturbations including slowed growth, gas vesicle biogenesis deficiency and morphologic abnormalities upon the overexpression of a single GTF - TBPd. These phenotypes were quantified and were attributed to a perturbation in the regulation of aconitase. Importantly, our results demonstrate why an experiment design as simple as a simple batch culture can be enormously informative of activities and interrelationships of a large fraction of all genes in a microbe. Halobacterium NRC-1 was grown in shaken (220RPM) complete medium liquid culture at 37°C in duplicate flasks. Samples were selected at 7 timepoints during the growth of this organism representing different phases of growth (e.g. early exponential, logrithmic, stationary etc.). RNA extractions were performed using the Stratagene Absolutely RNA Miniprep Kit and RNA quality checked with the Agilent Bioanalyzer and with Oligo Microarrays were fabricated at the Institute for Systems Biology Microarray Facility. The arrays contain 4 spots per unique 70-mer oligonucleotides for each of 2400 non-redundant genes in Halobacterium NRC-1 Labeling, hybridization and washing have been previously described (Baliga et al. 2002) with 10 μg of RNA from the sample and reference. RNA from the final time point of a replicate experiment was used as the reference. Bias in dye incorporation was accounted for by reversing the labeling dyes (dye-flip). Raw data was processed and converted into log10 ratios with lambda (λ) values determined by a maximum likelihood method.Baliga, N. S., Pan, M., Goo, Y. A., Yi, E. C., Goodlett, D. R., Dimitrov, K., Shannon, P., Aebersold, R., Ng, W. V. & Hood, L. (2002) Proc Natl Acad Sci U S A 99:14913-84.
2010-05-14 | E-GEOD-14832 | biostudies-arrayexpress