Global gene expression of Ruegeria pomeroyi strain DSS3 in response to glucose, ammonium, phosphate, or sulfate limitation
ABSTRACT: We used the previously designed oligonucleotide-based microarray (Burgmann et al. Environmental Microbiology 2007, 9: 2742-2755) to detect the transcripts of R. pomeroyi DSS-3 genes when the cells were cultured under steady-state carbon (glucose), nitrogen (ammonium), phosphorus (phosphate), or sulfur (sulfate) limitation. A total of 14 mRNA samples were hybridized to the arrays (three biological replicates from glucose, ammonium, phosphate, or sulfate limitation and one technical replicate each for ammonium or sulfate limitation)
Project description:We used the previously designed oligonucleotide microarrays (Bürgmann et al., 2007, Environmental Microbiology, 9: 2742-2755) to detect the mRNA transcripts of R. pomeroyi DSS-3 when the cells were cultured under steady-state conditions limited with ammonium (NH4Cl, 0.26 mM) but with an excess of D-ribose-5-phosphate (C5H9Na2O8P*2H2O, 0.5 mM), methylphosphonic acid (CH5PO3, 0.5 mM), or potassium phosphate (KH2PO4, 0.5 mM), or during ammonium excess (NH4Cl, 2.8 mM) but were limited with potassium phosphate (KH2PO4, 9.2 μM). A total of 13 microarray hybridizations were performed: three biological replicates each from ribose phosphate, methylphosphonate, or potassium phosphate excess growth regimes, three biological replicates from potassium phosphate limited growth regime, and one technical replicate for the potassium phosphate excess growth regime. Data for the technical replicates were averaged and combined, resulted in a total of 12 samples.
Project description:We used the previously designed oligonucleotide-based microarray (Burgmann et al. Environmental Microbiology 2007, 9: 2742-2755) to detect the transcripts of R. pomeroyi DSS-3 genes when the cells were cultured under steady-state carbon (glucose), nitrogen (ammonium), phosphorus (phosphate), or sulfur (sulfate) limitation. Overall design: A total of 14 mRNA samples were hybridized to the arrays (three biological replicates from glucose, ammonium, phosphate, or sulfate limitation and one technical replicate each for ammonium or sulfate limitation)
Project description:This study is measuring the steady-state levels of mRNA in wild-type Caulobacter crescentus grown in M2 defined medium containing either ammonium or nitrate as the sole nitrogen source. Four independent cultures of Caulobacter crecentus were grown in each of two medium conditions: M2(nitrate)glucose and M2(ammonium)glucose. Cultures in each medium type were grown to OD660=0.3 and RNA was isolated from each.
Project description:S. cerevisiae cells (homozygous deletion mutants of BY4743) grown in chemostats, sampled at steady state. Glucose and ammonium limitation, dilution rates 0.1 and 0.2 hr<sup>-1</sup>, gene deletions HO and HAP4 applied.
Project description:Nitrogen limitation is a major regulator to initiate lipid overproduction in oleaginous fungi. To examine the influence of nitrogen starvation, chemiostat cultures of R. toruloides in defined media with abundant ammonium (MM) or minute ammonium (MM-N) were performed to obtain steady-state samples. Then Illumina's digital gene expression (DGE) technology was used for high-throughput transcriptome profiling of these samples. Two samples cultured in minimum media with abundant ammonium (MM) or minute ammonium (MM-N)
Project description:Fatty acid synthesis is closely linked to nutrient availability and cellular energetic status. The committed step in fatty acid synthesis is the acetyl CoA carboxylase. Eukaryotes have two genes encoding acetyl CoA carboxylases, one encoding a cytosolic enzyme and another coding for a mitochondrial enzyme. They catalyze the synthesis of malonyl CoA in the cytosol and the mitochondria, respectively. While cytosolic malonyl CoA is the precursor for fatty acid synthesis, mitochondrial malonyl CoA controls the transfer of fatty acyl group into the mitochondria by inhibiting carnitine/palmitoyl transferase activity and thus, regulates β-oxidation. In Saccharomyces cerevisiae, β-oxidation is restricted to the peroxisomes, raising the question of the function of the mitochondrial isoform (HFA1). In this study, we replaced the cytosolic Acc1 with Hfa1 expressed in the cytosol by removing the mitochondrial leader peptide, under control of the HFA1 promoter. We studied fatty acid synthesis and transcription profiles in this strain during starvation for carbon or nitrogen, using glucose or ethanol as the carbon source. Under all the conditions studied, the key sensor of energetic status, Snf1, was activated, indicating active inhibition of fatty acid synthesis. The pool size of fatty acids was smaller when Acc1 was replaced with truncated Hfa1 for fatty acid synthesis. Yet, the transcription profiles were similar in both the cases. These results point towards the conclusion that Hfa1 is either catalytically less efficient or it is more sensitive to inhibition by Snf1. Gene expression from a strain of Saccharomyces cerevisiae where cytosolic fatty acid synthesis occurs by mitochondrial acetyl CoA carboxylase (without its mitochondrial leader peptide) is compared with that in a reference strain while growing in chemostats on carbon or nitrogen starvation using glucose or ethanol as the carbon source. There are two strains (reference or mutant), two carbon sources (glucose or ethanol) and two limitations (carbon or nitrogen), resulting in 8 comparisons. Each array was performed in duplicate, resulting in 16 CEL files. Growth was limited by either carbon or nitrogen. When carbon was the limited nutrient, we tested growth on either glucose or ethanol (both using ammonium sulfate as the nitrogen source). When ammonium sulfate was limiting, we used either glucose or ethanol as the carbon source.
Project description:Expression data for Desulfovibrio alaskensis strain G20 and mutants in regulator proteins grown on lactate sulfate media and then pelleted and transferred to another media when they reached stationary phase. The Choline mutant was transferred to lacte/sulfate minimal media and choline/sulfate minimal media. The LysX mutant was transferred to minimal media with lysine and rich media. G20 was transferred to minimal media, choline/sulfate minimal media, lactate/choline/sulfate minimal media, minimal media with lysine, and rich media. We aimed to confirm or expand the regulons of each of the transposon interupted regulator mutants and compare gene expression responses of the regulators in different growth conditions. 10 samples were collected: 2 regulator mutants (2 conditions each), Desulfovibrio alaskensis G20 (5 conditions), 2 replicates for G20 minimal media condition. Control sample -G20 rich media.
Project description:Wild type S. cerevisiae cells were grown under glucose or ammonium limitation in fully controlled aerobic chemostat cultures. At steady state, the limited nutrient was introduced into the growth medium in an impulse like manner to recover the medium to its non-limiting conditions. Samples were collected at steady state and following the impulse (20s, 40s, 60s, 8 min, 16 min, 24 min, 32 min, 1 hr, 2hr, 3hr, 4hr, 5hr, 7 hr) until the effect of the perturbation ceased to exist. The last sample was collected the second time the chemostat reached steady state.
Project description:Next generation sequencing was used to assess transcriptome changes in haploid U. maydis wild type and mutant strains grown under nitrogen-replete and low ammonium media. Overall design: Wild type and mutant strains were grown for 48 hours at 26 C, in microarray media ((6.25% Holliday Salt Solution (Holliday, 1974), 1% glucose, and 2% agar) with either 30 mM Glutamine/50 mM Ammonium sulfate (Hi) or 50 uM Ammonium sulfate (Lo)
Project description:Response of Saccharomyces cerevisiae to Ammonium, L-alanine, or L-glutamine Limitation. The protrotophic laboratory strain CEN.PK113-7D (MAT a) was grown in laboratory fermentors with a working volume of 1 litre at dilution rate (D) of 0.20 per hour (in triplicate for each nitrogen limited condition). At steady state, samples from each of the 12 continuous cultures were taken and cooled below 2 degree C within ten seconds by mixing 40% sample and 60% crushed ice.