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Series GSE17515 Query DataSets for GSE17515
Status Public on May 26, 2010
Title Coordination of frontline defense mechanisms under severe oxidative stress.
Platform organism Halobacterium salinarum NRC-1
Sample organism Halobacterium salinarum
Experiment type Expression profiling by array
Summary 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.

 
Overall design 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.
 
Contributor(s) Kaur A, Van PT, Busch CR, Robinson CK, Pan M, Pang WL, Reiss D, DiRuggiero J, Baliga NS
Citation(s) 20664639
Submission date Aug 05, 2009
Last update date Jan 15, 2017
Contact name Dan Tenenbaum
Organization name Institute for Systems Biology
Street address 1441 N. 34th St.
City Seattle
State/province WA
ZIP/Postal code 98103
Country USA
 
Platforms (1)
GPL3739 ISB Halobacterium Spotted Microarray
Samples (202)
GSM435471 Coordination of frontline defense mechanisms under severe oxidative stress. Array 10311
GSM435472 Coordination of frontline defense mechanisms under severe oxidative stress. Array 10312
GSM435473 Coordination of frontline defense mechanisms under severe oxidative stress. Array 10313
Relations
BioProject PRJNA118789

Download family Format
SOFT formatted family file(s) SOFTHelp
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Series Matrix File(s) TXTHelp

Supplementary file Size Download File type/resource
GSE17515_RAW.tar 222.7 Mb (http)(custom) TAR (of CSV)
Processed data included within Sample table

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