Transcription profiling by array of Streptomyces venezuelae wild type and GlnR and GlnRII mutant strains under varying conditions of nitrogen limitation
Ontology highlight
ABSTRACT:
ORGANISM(S): Streptomyces venezuelae
SUBMITTER: Steven Pullan
PROVIDER: E-MEXP-2684 | biostudies-arrayexpress |
REPOSITORIES: biostudies-arrayexpress
Similar Datasets
Project description:ChIP-chip analysis of GlnR-FLAG binding sites in Streptomyces venezuelae under varying conditions of nitrogen availibility
2011-04-20 | E-MEXP-2933 | biostudies-arrayexpress
Project description:Our approach for the identification and quantification of growth control by the components of yeast cells relies on two complementary screens: In the first, growth rate is changed and the effect on the concentration of cell components is measured (Castrillo et al. 2007, Genome Biology, 6,4). In the second, the concentration of the components is changed (by reducing gene copy number) and the effect on growth rate is measured (Delneri et al., 2008, Nat Gen, 40, 113). The heterozygous deletant (hemizygote) library we use is composed of diploid mutants each lacking one copy of a different gene (Giaever et al., 2002, Nature, 418, 387). When such a pool of mutants is grown in competition, some will grow slower than the others due to their particular mutation. Over time, the proportion of these mutants in the population will decrease a phenotype termed `haploinsufficient. Conversely, some mutants will have a growth-rate advantage and so will increase their proportion in the population; we call these strains `haploproficient. Screening a pool of hemizygotes for their haploinsufficiency (HI)/haploproficiency (HP) phenotypes thus identifies cellular components that have high flux control (HFC) over growth rate. We found that genes that are major controllers of growth rate under nutrient-limitation are not, themselves, subject to growth rate control of their transcription. In this study we have investigated the generality of this rule, first by identifying HFC genes in turbidostat culture, where biomass concentration sets the rate of nutrient addition, growing at the maximum rate (mmax=0.32h-1) permitted by the complex defined medium (FPM) employed. And to study growth-rate effects, competition experiments were performed at higher growth rates (D=0.2h-1 and 0.3h-1) in nitrogen-limited chemostats and, to control for the effect of nitrogen limitation, in FPM using a chemostat at D=0.3h-1 (Pir et al., manuscript in preparation)
2010-12-01 | E-TABM-892 | biostudies-arrayexpress
Project description:Changes in protein synthesis and degradation rates, transcript, protein and phytohormone abundance of 99 targets using qPCR and LC-MS parallel reaction monitoring (PRM) were measured in the transitions between optimal growth conditions (homeostasis), fully induced pattern triggered immunity (PTI) and back in Arabidopsis thaliana, chronologically. Protein turnover rates play an important role in the tryptophan and glucosinolate biosynthesis and photosynthesis associated (PAP) proteins. Most transcripts returned to normal levels 3 to 16 hours post elicitation, while protein levels remained at fully induced PTI levels up to 16 hours into the transitory phase back to optimal growth. Same measurements in the myc234 background revealed an important role of these transcription factors in the immune response including effects on protein turnover rates.
2023-10-13 | PXD041215 | Pride
Project description:Genome-wide gene responses in a transgenic rice line carrying the maize resistance gene Rxo1 to the rice bacterial streak pathogen, Xanthomonas oryzae pv. oryzicola; Non-host resistance in rice to its bacterial pathogen, Xanthomonas oryzae pv. oryzicola (Xoc), mediated by a maize NBS-LRR type R gene, Rxo1 shows a typical hypersensitive reaction (HR) phenotype, but the molecular mechanism(s) underlying this type of non-host resistance remain largely unknown. Results A microarray experiment was performed to reveal the molecular mechanisms underlying HR of rice to Xoc mediated by Rxo1 using a pair of transgenic and non-transgenic rice lines. Our results indicated that Rxo1 appeared to function in the very early step of the interaction between rice and Xoc, and could specifically activate large numbers of genes involved in signaling pathways leading to HR and some basal defensive pathways such as SA and ET pathways. In the former case, Rxo1 appeared to differ from the typical host R genes in that it could lead to HR without activating NDR1. In the latter cases, Rxo1 was able to induce a unique group of WRKY TF genes and a large set of genes encoding PPR and RRM proteins that share the same G-box in their promoter regions with possible functions in post-transcriptional regulation. In conclusion, Rxo1, like most host R genes, was able to trigger HR against Xoc in the heterologous rice plants by activating multiple defensive pathways related to HR, providing useful information on the evolution of plant resistance genes. Maize non-host resistance gene Rxo1 could trigger the pathogen-specific HR in heterologous rice, and ultimately leading to a localized programmed cell death which exhibits the characteristics consistent with those mediated by host resistance genes, but a number of genes encoding pentatricopeptide repeat and RNA recognition motif protein were found specifically up-regulated in the Rxo1 mediated disease resistance. These results add to our understanding the evolution of plant resistance genes. Experiment Overall Design: All inoculated flag leaves from three plants of 9804-Rxo1 and 9804 were collected two days post-inoculation (dpi), and the flag leaves from three non-inoculated check plants of 9804-Rxo1 and 9804 were also sampled at the same time point as control. The flag leaves from non-inoculated check plants of 9804 were sampled at the same time point as control: 9804-Rxo1 (3-replications), XOC - time: 2 dpi(3-replications); 9804-Rxo1 (3-replications); 9804, XOC - time: 2 dpi(3-replications) 9804. 2 sets of separately normalized data: 9804-Rxo1 and 9804.
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Project description:Accessing the natural genetic diversity of species unveils hidden genetic traits, clarifies gene functions, and allows assessment of the generalizability of laboratory findings. One notable discovery made in Saccharomyces cerevisiae natural isolates is frequent (~20%) aneuploidy – an imbalance in chromosome copy numbers – that appears to contradict the significant fitness costs and transient nature reported for lab-engineered aneuploids. Here, we generated a proteomic resource and merged it with genomic and transcriptomic data for 796 euploid and aneuploid natural isolates. We found that natural and lab-generated aneuploids differ specifically at the proteome. In lab-generated aneuploids, some proteins, especially protein complex subunits, show reduced expression, yet the overall protein levels correspond to the aneuploid gene dosage. By contrast, in natural isolates, more than 70% of proteins encoded on aneuploid chromosomes are dosage-compensated, with average protein levels being shifted towards the euploid state chromosome-wide. At the molecular level, we detect an induction of structural components of the proteasome, increased levels of ubiquitination, and reveal an interdependency of protein turnover rates and attenuation. Our study thus highlights the role of protein turnover in mediating aneuploidy tolerance, and demonstrates the utility of exploiting the natural diversity of species to reach generalizable molecular insights into complex biological processes. This resource provides the SILAC dataset from this work.
2024-03-13 | PXD048219 | Pride
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2011-08-29 | E-MEXP-3320 | biostudies-arrayexpress
Project description:Investigation of lipid metabolism as a function of three experimental factors: 1) aerobicity (aerobic vs anaerobic, or 'A' vs 'O'), 2) nutrient limitation (carbon vs nitrogen limitation, or 'C' vs 'N'), 3) temperature (30C vs 15C, or 'T' vs 't') using a full factorial design.
2013-01-31 | E-MEXP-3704 | biostudies-arrayexpress
Project description:This SuperSeries is composed of the following subset Series: GSE40336: Effect of Acetominophen on Rat Primary Hepatocytes. GSE40337: Effect of Dioctyl Phthalate on Rat Primary Hepatocytes. GSE40338: Effect of Sodium Valproate on Rat Primary Hepatocytes. GSE40339: Effect of Phenobarbital on Rat Primary Hepatocytes. GSE40340: Effect of Beta-Naphthoflavone on Rat Primary Hepatocytes. GSE40341: Effect of Chlorpromazine HCl on Rat Primary Hepatocytes. GSE40342: Effect of Diisononyl Phthalate on Rat Primary Hepatocytes. GSE40344: Effect of Clofibrate on Rat Primary Hepatocytes. GSE40346: Effect of WY-14643 on Rat Primary Hepatocytes. GSE40347: Effect of Methapyrilene on Rat Primary Hepatocytes. Refer to individual Series
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Project description:Saccharomyces cerevisiae cells were exposed to a copper chelator (100uM BCS) for 48 hours. Samples were compared to the zero hour timepoint at 0.5, 1, 2, 3, 4, 24 and 48 hours.
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Project description:Wild type versus reference pool. Reference pools from either the CuSO4 or BCS timecourse were compared with wildtype cells taken from mid-log cultures.
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