Halobacterium NRC-1 ura3 parent strain and VNG1451C deletion mutant in response to growth in rich medium
Ontology highlight
ABSTRACT:
ORGANISM(S): Halobacterium sp. NRC-1
SUBMITTER: Baliga Nitin S.
PROVIDER: E-GEOD-13531 | biostudies-arrayexpress |
REPOSITORIES: biostudies-arrayexpress
Publications
A single transcription factor regulates evolutionarily diverse but functionally linked metabolic pathways in response to nutrient availability.
Schmid Amy K AK Reiss David J DJ Pan Min M Koide Tie T Baliga Nitin S NS
Molecular systems biology 20090616
During evolution, enzyme-coding genes are acquired and/or replaced through lateral gene transfer and compiled into metabolic pathways. Gene regulatory networks evolve to fine tune biochemical fluxes through such metabolic pathways, enabling organisms to acclimate to nutrient fluctuations in a competitive environment. Here, we demonstrate that a single TrmB family transcription factor in Halobacterium salinarum NRC-1 globally coordinates functionally linked enzymes of diverse phylogeny in respons ...[more]
Similar Datasets
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. Halobacterium salinarum NRC-1 (ATCC700922) ura3 parent and VNG1451C strains were grown in complete defined medium (CDM; 20 amino acids at concentrations defined by Shand and Perez, 1999. NaCl 250g/L, MgSO4 20 g/L, KCl 1 g/L, NaH2PO4 0.167mM, Biotin 0.02mM, Thiamin 0.015mM, Folic acid 0.0113 mM, MnSO4 0.01mM, FeSO4, 0.01mM, glucose added at 10% w/v where indicated in sample files) at 37ºC under full-spectrum white light. Biological replicate samples were removed throughout the growth curve at early log, mid log, and stationary phase to measure genome-wide transcription.
2010-05-06 | E-GEOD-13529 | biostudies-arrayexpress
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. Halobacterium salinarum NRC-1 (ATCC700922) ura3 parent and VNG1451C strains were grown in rich medium (CM, 250 NaCl, 20 g/L MgSO4?7H2O, 3 g/L sodium citrate, 2 g/L KCl, 10 g/L peptone) with or without varying concentrations of glucose or glycerol at 37ºC under full-spectrum white light. The cells were cross-linked with 1.2% formaldehyde, then lysed and DNA sheared via sonication. Next cleared cell lysate was subject to immunoprecipitation against an anti-myc antibody. Protein-DNA complexes were purified and DNA was isolated after protease and RNAase treatment. DNA was amplified using universal linkers, labeled directly using Kreatech 547 and 647 dyes. Samples were grown in biological duplicate. Each DNA sample was hybridized against 2 microarrays as dyefilps. At least two experiments (including biological duplicates) were carried out.
2010-05-06 | E-GEOD-13498 | biostudies-arrayexpress
Project description:A 50ml culture of Halobacterium NRC-1 knockout strain delta-ura3 with additional in-frame gene deletion of vng0019h was grown to mid-log phase in a 125ml flask in rich media under varying oxygen and light conditions. Low and high light indicate growth in a painted flask versus growth in a standard clear flask under constant standard incubator illumination, respectively. Low and high oxygen indicate shaking in a stoppered flask at 100RPM agitation or shaking in a non-stoppered flask at 220RPM, respectively. Each of the four possible pairwise environemental combinations were assayed : High-oxygen/high-light, Low-oxygen/high-light, High-oxygen/low-light and Low-oxygen/low-light. 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. 4 samples were analyzed in duplicate (8 total microarrays) as dye-flips.
2010-05-26 | E-GEOD-7737 | biostudies-arrayexpress
Project description:This SuperSeries is composed of the following subset Series: GSE7714: Halobacterium NRC-1 oxygen, light and phr1 perturbation GSE7715: Halobacterium NRC-1 oxygen, light and ura3 perturbation GSE7716: Halobacterium NRC-1 oxygen, light and phr1/phr2 perturbation GSE7717: Halobacterium NRC-1 oxygen, light and bop perturbation GSE7718: Halobacterium NRC-1 oxygen, light and phr2 perturbation GSE7719: Halobacterium NRC-1 oxygen, light and sop2 perturbation GSE7720: Halobacterium NRC-1 oxygen, light and afsQ2 perturbation GSE7721: Halobacterium NRC-1 oxygen, light and htlD perturbation GSE7722: Halobacterium NRC-1 oxygen, light and vng0750C perturbation GSE7723: Halobacterium NRC-1 oxygen, light and boa1 perturbation GSE7724: Halobacterium NRC-1 oxygen, light and ark perturbation GSE7725: Halobacterium NRC-1 oxygen, light and boa4 perturbation GSE7726: Halobacterium NRC-1 oxygen, light and htr1 perturbation GSE7727: Halobacterium NRC-1 oxygen, light and kinA2 perturbation GSE7728: Halobacterium NRC-1 oxygen, light and htr8 perturbation GSE7729: Halobacterium NRC-1 oxygen and light perturbation GSE7730: Halobacterium NRC-1 oxygen, light and phoR perturbation GSE7731: Halobacterium NRC-1 oxygen, light and htr2 perturbation GSE7732: Halobacterium NRC-1 oxygen, light and vng1296C perturbation GSE7733: Halobacterium NRC-1 oxygen, light and vng2334C perturbation GSE7734: Halobacterium NRC-1 oxygen, light and zim perturbation GSE7735: Halobacterium NRC-1 oxygen, light and kinA2 perturbation, experiment 2 GSE7736: Halobacterium NRC-1 oxygen, light and sop2 perturbation, experiment 2 GSE7737: Halobacterium NRC-1 oxygen, light and vng0019h perturbation GSE7738: Halobacterium NRC-1 oxygen, light and gap perturbation Refer to individual Series
2008-01-02 | E-GEOD-7740 | biostudies-arrayexpress
Project description:A 50ml culture of Halobacterium NRC-1 knockout strain delta-ura3 with additional in-frame gene deletions of phr1 and phr2 was grown to mid-log phase in a 125ml flask in rich media under varying oxygen and light conditions. Low and high light indicate growth in a painted flask versus growth in a standard clear flask under constant standard incubator illumination, respectively. Low and high oxygen indicate shaking in a stoppered flask at 100RPM agitation or shaking in a non-stoppered flask at 220RPM, respectively. Each of the four possible pairwise environemental combinations were assayed : High-oxygen/high-light, Low-oxygen/high-light, High-oxygen/low-light and Low-oxygen/low-light. 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. Keywords: environmental response, genetic perturbation 4 samples were analyzed in duplicate (8 total microarrays) as dye-flips.
2008-01-03 | E-GEOD-7716 | biostudies-arrayexpress
Project description:A 50ml culture of Halobacterium NRC-1 knockout strain delta-ura3 with additional in-frame gene deletion of bop was grown to mid-log phase in a 125ml flask in rich media under varying oxygen and light conditions. Low and high light indicate growth in a painted flask versus growth in a standard clear flask under constant standard incubator illumination, respectively. Low and high oxygen indicate shaking in a stoppered flask at 100RPM agitation or shaking in a non-stoppered flask at 220RPM, respectively. Each of the four possible pairwise environemental combinations were assayed : High-oxygen/high-light, Low-oxygen/high-light, High-oxygen/low-light and Low-oxygen/low-light. 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. 4 samples were analyzed in duplicate (8 total microarrays) as dye-flips.
2010-05-26 | E-GEOD-7717 | biostudies-arrayexpress
Project description:A 50ml culture of Halobacterium NRC-1 knockout strain delta-ura3 with additional in-frame gene deletion of afsQ2 was grown to mid-log phase in a 125ml flask in rich media under varying oxygen and light conditions. Low and high light indicate growth in a painted flask versus growth in a standard clear flask under constant standard incubator illumination, respectively. Low and high oxygen indicate shaking in a stoppered flask at 100RPM agitation or shaking in a non-stoppered flask at 220RPM, respectively. Each of the four possible pairwise environemental combinations were assayed : High-oxygen/high-light, Low-oxygen/high-light, High-oxygen/low-light and Low-oxygen/low-light. 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. 4 samples were analyzed in duplicate (8 total microarrays) as dye-flips.
2010-05-26 | E-GEOD-7720 | biostudies-arrayexpress
Project description:A 50ml culture of Halobacterium NRC-1 knockout strain delta-ura3 with additional in-frame gene deletion of vng0750C was grown to mid-log phase in a 125ml flask in rich media under varying oxygen and light conditions. Low and high light indicate growth in a painted flask versus growth in a standard clear flask under constant standard incubator illumination, respectively. Low and high oxygen indicate shaking in a stoppered flask at 100RPM agitation or shaking in a non-stoppered flask at 220RPM, respectively. Each of the four possible pairwise environemental combinations were assayed : High-oxygen/high-light, Low-oxygen/high-light, High-oxygen/low-light and Low-oxygen/low-light. 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. 4 samples were analyzed in duplicate (8 total microarrays) as dye-flips.
2010-05-26 | E-GEOD-7722 | biostudies-arrayexpress
Project description:A 50ml culture of Halobacterium NRC-1 knockout strain delta-ura3 with additional in-frame gene deletion of htlD was grown to mid-log phase in a 125ml flask in rich media under varying oxygen and light conditions. Low and high light indicate growth in a painted flask versus growth in a standard clear flask under constant standard incubator illumination, respectively. Low and high oxygen indicate shaking in a stoppered flask at 100RPM agitation or shaking in a non-stoppered flask at 220RPM, respectively. Each of the four possible pairwise environemental combinations were assayed : High-oxygen/high-light, Low-oxygen/high-light, High-oxygen/low-light and Low-oxygen/low-light. 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. 4 samples were analyzed in duplicate (8 total microarrays) as dye-flips.
2010-05-26 | E-GEOD-7721 | biostudies-arrayexpress
Project description:A 50ml culture of Halobacterium NRC-1 knockout strain delta-ura3 with additional in-frame gene deletion of htr1 was grown to mid-log phase in a 125ml flask in rich media under varying oxygen and light conditions. Low and high light indicate growth in a painted flask versus growth in a standard clear flask under constant standard incubator illumination, respectively. Low and high oxygen indicate shaking in a stoppered flask at 100RPM agitation or shaking in a non-stoppered flask at 220RPM, respectively. Each of the four possible pairwise environemental combinations were assayed : High-oxygen/high-light, Low-oxygen/high-light, High-oxygen/low-light and Low-oxygen/low-light. 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. 4 samples were analyzed in duplicate (8 total microarrays) as dye-flips.
2010-05-26 | E-GEOD-7726 | biostudies-arrayexpress