Transcriptional profiling of rice salt sensitive 1 (rss1) mutant
Ontology highlight
ABSTRACT:
ORGANISM(S): Oryza sativa
SUBMITTER: Daisuke Ogawa
PROVIDER: E-GEOD-27884 | biostudies-arrayexpress |
REPOSITORIES: biostudies-arrayexpress
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Project description:Transcriptional profiling of WT and rss3 root tips, grown in the presense or absense of 100 mM NaCl for 3 days. WT (-NaCl), WT (+NaCl), rss3 (-NaCl), rss3 (+NaCl). Three biological replicates.
2012-10-15 | E-GEOD-41442 | biostudies-arrayexpress
Project description:Boron (B) is an essential micronutrient for vascular plants. Boron works to build the cell wall structure by forming borate ester cross-links with pectin, and the deficiency of this element brings about oxidative damage and cell death. However, the process via which B deficiency leads to such serious damage has not been well understood. We investigated the temporal changes in metabolism of B-deprived cultured tobacco (Nicotiana tabacum) BY-2 cells by analyzing their gene expression using cDNA microarray. Three-day-old cells were deprived of B by washing with and transferred to B-free growth media ("-B" cells). Cells similarly treated with standard growth media were employed as a control for the effects of mechanical stress ("+B cells"). Cells were sampled at 1, 3, 6, 12 and 36 h after transfer to the B-free or standard media. Cells without washing treatment were also included in the analysis ("before-treatment cells"). Two independent sets of samples were analyzed (replicate 1 and 2).
2012-05-04 | E-GEOD-37649 | biostudies-arrayexpress
Project description:Samples GSM206658-GSM206693: Acquired Stress resistance in S. cerevisiae: NaCl primary and H2O2 secondary Transcriptional timecourses of yeast cells exposed to 0.7M NaCl alone, 0.5mM H2O2 alone, or 0.5mM H2O2 following 0.7M NaCl, all compared to an unstressed sample. Repeated using msn2∆ strain. Samples GSM291156-GSM291196: Transcriptional response to stress in strains lacking MSN2 and/or MSN4 Transcriptional timecourses of yeast cells (WT, msn2∆, msn4∆, or msn2∆msn4∆) exposed to 0.7M NaCl for 45 minutes or 30-37˚C Heat Shift for 15 min compared to an unstressed sample of the same strain. Keywords: Stress Response
2008-09-05 | GSE8335 | GEO
Project description:Background The catabolite control protein A (CcpA) is a member of the LacI/GalR family of transcriptional regulators controlling carbon-metabolism pathways in low-GC Gram positive bacteria. It functions as a catabolite repressor or activator, allowing the bacteria to utilize the preferred carbon source over secondary carbon sources. This study is the first CcpA-dependent transcriptome and proteome analysis in S. aureus wild type and ccpA-deleted mutant, focussing on short-time effects of glucose under stable pH conditions. Results The addition of glucose to exponentially growing S. aureus increased enzymes of glycolytic pathway, indicating a higher glycolytic activity, while proteins required for the complete oxidation in the TCA cycle were repressed via CcpA. Phosphotransacetylase and acetate kinase, converting acetylCoA to acetate with a concomitant substrate-level phosphorylation were neither regulated by glucose nor by CcpA. Most CcpA directly repressed genes were involved in utilization of amino acids as secondary carbon sources. More genes were found to be differentially expressed by CcpA in a glucose-independent manner than in the classical, glucose dependent way, suggesting that glucose-independent regulation by CcpA may be of particular importance in S. aureus. In the presence of glucose, CcpA was found to regulate expression of genes involved in metabolism, but that of genes coding for virulence determinants. Conclusions This study identified the CcpA regulon of exponentially growing S. aureus, for the first time. As in other bacteria, the CcpA-regulon of S. aureus comprised a large amount of metabolic genes but also some 50 genes associated with virulence. CcpA seemed to work in a glucose- as well as glucose-independent way. The transcriptomes of strain Newman and its isogenic ccpA-deleted mutant were determined in early exponential growth and 30 min after the addition of 10 mM glucose, under controlled pH conditions. In the absence of glucose, the wild type grew slightly faster than the mutant, reaching an OD600 of 1 approximately 20 min earlier than the mutant. Adding 10 mM glucose at OD600 1 increased the growth rate of the wild type but had only a minor effect on that of the mutant. 60 min after glucose addition, glucose was depleted down to 0.3 mM by the wild type, while still 3 mM glucose was left in the culture of the mutant. Despite increased glucose consumption rates in the wild type, acetate production was only slightly enhanced compared to the mutant. No lactate was excreted at any time point sampled. Acidification of the medium upon glucose metabolism was prevented by buffering, maintaining a pH of 7.5 for both strains and under both growth conditions for at least 2 h after glucose addition, allowing to rule out any pH effects.
2010-06-24 | E-GEOD-12614 | biostudies-arrayexpress
Project description:Guanosine 3 ,5 -bispyrophosphate (ppGpp), also known as ‘‘magic spot,’’ has been shown to bind prokaryotic RNA polymerase to down-regulate ribosome production and increase transcription of amino acid biosynthesis genes during the stringent response to amino acid starvation. Because many environmental growth perturbations cause ppGpp to accumulate, we hypothesize ppGpp to have an overarching role in regulating the genetic program that coordinates transitions between logarithmic growth (feast) and growth arrest (famine). We used the classic glucose-lactose diauxie as an experimental system to investigate the temporal changes in transcription that accompany growth arrest and recovery in wildtype Escherichia coli and in mutants that lack RelA (ppGpp synthetase) and other global regulators, i.e., RpoS and Crp. When cultured on a mixture of glucose and lactose, E. coli grows preferentially on glucose until it is exhausted, resulting in growth arrest while the cells adjust to growth on lactose, i.e., diauxie. Diauxie was delayed in the relA mutant and was accompanied by a 15% decrease in the number of carbon sources used and a 3-fold overall decrease in the induction of RpoS and Crp regulon genes. Thus the data significantly expand the previously known role of ppGpp and support a model wherein the ppGpp-dependent redistribution of RNA polymerase across the genome is the driving force behind control of the stringent response, general stress response, and starvation-induced carbon scavenging. Our conceptual model of diauxie describes these global control circuits as dynamic, interconnected, and dependent upon ppGpp for the efficient temporal coordination of gene expression that programs the cell for transitions between feast and famine. E. coli MG1655 and isogenic mutants were cultured in a 2 l Biostat B fermentor (B. Braun Biotech International) containing 1 liter of Morpholinepropanesulfonic acid (MOPS) minimal medium with 0.5 g/l of glucose and 1.5 g/l of lactose. The temperature was maintained at 37 ºC and pH was kept constant at 7.2 by the addition of 2 M NaOH. The dissolved oxygen level was maintained above 20% of saturation by adjusting the agitation speeds in the range of 270-500 rpm with fixed 1 l/min air flow.
2007-03-17 | E-GEOD-7265 | biostudies-arrayexpress
Project description:Total RNA was isolated with RNAiso regent (Takara) from 12-day-old seedlings of the areb1 areb2 abf3 triple mutant and WT plants grown on GM agar plates with stress treatment of 250 mM NaCl for 6 h.
2010-07-05 | E-MEXP-2293 | biostudies-arrayexpress
Project description:To identify mediators of the osmotic stress response in Mycobacterium tuberculosis (Mtb), we performed transcriptional profiling of WT CDC1551 following treatment with 140 mM NaCl for 1 hr relative to an untreated control. 140 mM NaCl was chosen to reflect the approximate osmolarity of human plasma (i.e., 280 mOsm/L), which may be relevant during the course of infection.
2013-11-15 | GSE50159 | GEO
Project description:Promoters of many G2/M phase-specific genes in plants contain mitosis-specific activator (MSA) elements, which act as G2/M phase-specific enhancers and bind with R1R2R3-Myb transcription factors. A least three R1R2R3-Myb proteins are expressed in tobacco (Nicotiana tabacum). To examine the genome-wide effects of NtmybA2 overexpression, we constructed transgenic tobacco BY-2 cell lines overexpressing full-length NtmybA2 protein. In addition, we generated transgenic BY-2 cell lines that overexpress truncated hyperactive form of NtmybA2 (NtmybA2âC) lacking its C-terminal region which negatively regulates its own activity for transcriptional activation. We used a custom-made 16K cDNA microarray for comparative transcriptome analysis of these transgenic tobacco BY-2 cell lines. As control sample, BY-2 cells transformed with empty vector pPZP-35S were used. The transgenic cell lines were analyzed during stationary phase (i.e. day 7-8 after subculture into fresh media). Keywords: Genetic modification 1. pPZP-35S vector control, 2. NtmybA2 overexpressor, 3. C-truncated NtmybA2 (NtmyA2âC) overexpressor
2010-05-22 | E-GEOD-14251 | biostudies-arrayexpress
Project description:Tobacco BY-2 cells can be highly synchronized by treatment with an inhibitor of DNA synthesis, aphidicolin. For comprehensive understanding of cell cycle-regulated gene expression in tobacco, microarray analysis was conducted in synchronized cultures of BY-2 cells. Cells were treated with aphidicolin for 24 hours to block the entry into and progression through the S phase. After release from the aphidicolin block, cells were sampled every 2 h from 0â16 h. cDNA probes prepared from these samples were hybridised to a custom-made16K microarray. We performed this procedure twice independently to identify transcripts that reproducibly showed similar cell cycle-regulated expression. A total of 883 putative cell cycle-regulated transcripts were identified from 16,896 duplicated spots on the microarrays. These transcripts could be categorised into 10 classes on the basis of transcript expression patterns in the cell cycle. Keywords: time course Synchronization experiments were repeated twice (experiments A and B). In each experiment, cells were sampled every 2 h during the culture periods (0-16 h), and used for microarray analysis.
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Project description:We performed a transcriptome analysis on the meristematic root tissue from the loss-of-function line an3 and WT plants.
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