Ontology highlight
ABSTRACT:
PROVIDER: PRJEB43656 | ENA |
REPOSITORIES: ENA
Dataset's files
| Action | DRS | |||
|---|---|---|---|---|
| ERR5463530_1.fastq.gz | Fastqsanger.gz | |||
| ERR5463530_2.fastq.gz | Fastqsanger.gz | |||
| ERR5463540_1.fastq.gz | Fastqsanger.gz | |||
| ERR5463540_2.fastq.gz | Fastqsanger.gz | |||
| ERR5463550_1.fastq.gz | Fastqsanger.gz |
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Project description:Pseudomonas aeruginosa under carbon starvation stress
| PRJNA550173 | ENA
Project description:Glucose is a widely used carbon source in laboratory practice to culture Aspergillus fumigatus, however, glucose availability is often low in its “natural habitats” including the human body. We used a physiological–transcriptomical approach to reveal differences between A. fumigatus Af293 cultures incubated on glucose, glucose and peptone, peptone (carbon limitation), or without any carbon source (carbon starvation). Autolytic cell wall degradation was upregulated by both carbon starvation and limitation. The importance of autolytic cell wall degradation in adaptation to carbon stress was also highlighted by approximately 12.4% of the A. fumigatus genomes harbor duplication of genes involved in N-acetyl glucosamine utilization. Glucose withdrawal increased redox imbalance, altered both the transcription of antioxidative enzyme genes and oxidative stress tolerance, downregulated iron acquisition, but upregulated heme protein genes. Transcriptional activity of the Gliotoxin cluster was low in all experiments, while the Fumagillin cluster showed substantial activity both on glucose and under carbon starvation, and the Hexadehydro-astechrome cluster only on glucose. We concluded that glucose withdrawal substantially modified the physiology of A. fumigatus including processes that contribute to virulence. This may explain the challenge of predicting the in vivo behavior of A. fumigatus based on data from glucose rich cultures.
2022-12-09 | GSE216000 | GEO
Project description:Rice blast is the most threatening disease to cultivated rice worldwide. Magnaporthe oryzae, its causal agent is likely to encounter environmental challenges during invasive growth in the host plants that require shifts in gene expression to establish a compatible interaction. Here, we tested the hypothesis that M. oryzae have similar gene expression patterns in planta, versus during in vitro stresses. Gene expression data was collected from in vitro experiments of heat shock, oxidative burst, and three different types of nutrient starvation. These data were compared to fungal gene expression during the invasive growth phase in compatible interactions on two grass hosts, rice and barley. We have identified 4,973 differentially expressed genes, from which 1,909 genes showed similar regulation patterns between at least one of the in vitro stresses and rice and/or barley. Hierarchical clustering of these 1,909 genes showed three major clusters in which growth in planta conditions closely grouped with the starving nutrient conditions. Out of these 1,909 genes, 55 and 129 genes were induced and repressed in all seven treatments, respectively. The functional categorization of those 55 induced genes revealed that most of them are either related to carbon metabolism, membrane proteins, or are involved in oxidoreduction reactions. The 129 repressed genes are putatively involved in vesicle trafficking, signal transduction, nitrogen metabolism, or molecular transport. These findings indicated that M. oryzae is likely coping with nutrient deprived environments in its hosts during the invasive growth stage about 72 hours post-inoculation, and not as much with host defense responses, or a temperature stress. Eight M. oryzae treatments: mycelia grown in liquid complete medium (set as the control); 72 hours post-incoulation (hpi) in rice leaves; 72 hours post-incoulation in barley leaves; mycelia under heat shock; mycelia under oxidative stress; mycelia under minimal medium; mycelia under nitrogen starvation; mycelia under carbon starvation. Three biological replicates had their total RNA pulled after RNA extraction. Dye-swaps used as technical replicates.
2011-01-24 | E-GEOD-21908 | biostudies-arrayexpress
Project description:Adaptation of Lactococcus lactis towards progressive carbon starvation is mediated by three different types of transcriptomic responses: i) global responses, i.e. general decrease of functions linked to bacterial growth and lack of induction of the general stress response, ii) specific responses functionally related to glucose exhaustion, i.e. under expression of central metabolism genes, induction of alternative sugars transport and metabolism genes, induction of arginine deiminase pathway genes and iii) other responses never described previously during carbon starvation. Keywords: stress response, time course
2008-02-23 | GSE5761 | GEO
Project description:Cultivation methods used to investigate microbial calorie restriction often result in carbon and energy starvation. This study aims to dissect cellular responses to calorie restriction and starvation in Saccharomyces cerevisiae by using retentostat cultivation. In retentostats, cells are continuously supplied with a small, constant carbon and energy supply, sufficient for maintenance of cellular viability and integrity but insufficient for growth. When glucose-limited retentostats cultivated under extreme calorie restriction were subjected to glucose starvation, calorie-restricted and glucose-starved cells were found to share characteristics such as increased heat-shock tolerance and expression of quiescence-related genes. However, they also displayed strikingly different features. While calorie-restricted yeast cultures remained metabolically active and viable for prolonged periods of time, glucose starvation resulted in rapid consumption of reserve carbohydrates, population heterogeneity due to appearance of senescent cells and, ultimately, loss of viability. Moreover, during starvation, calculated rates of ATP synthesis from storage carbohydrates were 2-3 orders of magnitude lower than steady-state ATP-turnover rates calculated under extreme calorie restriction in retentostats. Stringent reduction of ATP turnover during glucose starvation was accompanied by a strong down-regulation of genes involved in protein synthesis. These results demonstrate that extreme calorie restriction and carbon starvation represent different physiological states in S. cerevisiae.
2011-08-16 | GSE22602 | GEO
Project description:Abiotic stress causes disturbances in the cellular homeostasis. Re-adjustment of balance in carbon, nitrogen and phosphorus metabolism therefore plays a central role in stress adaptation. However, it is currently unknown which parts of the primary cell metabolism follow common patterns under different stress conditions and which represent specific responses. To address these questions, changes in transcriptome, metabolome and ionome were analyzed in maize source leaves from plants suffering low temperature, low nitrogen (N) and low phosphorus (P) stress. The selection of maize as study object provided data directly from an important crop species and the so far underexplored C4 metabolism. Growth retardation was comparable under all tested stress conditions. The only primary metabolic pathway responding similar to all stresses was nitrate assimilation, which was down-regulated. The largest group of commonly regulated transcripts followed the expression pattern: down under low temperature and low N, but up under low P. Several members of this transcript cluster could be connected to P metabolism and correlated negatively to different phosphate concentration in the leaf tissue. Accumulation of starch under low temperature and low N stress, but decrease in starch levels under low under low P conditions indicated that only low P treated leaves suffered carbon starvation. In conclusion, maize employs very different strategies for management of nitrogen and phosphorus metabolism under stress. While nitrate assimilation was regulated depending on demand by growth processes, phosphate concentrations changed depending on availability, thus building up reserves under excess conditions. Carbon and energy metabolism of the C4 maize leaves were particularly sensitive to P starvation.
2013-05-15 | GSE46704 | GEO
Project description:Here we used mass spectrometry-based proteomics technology to explore SEPs with potential cellular stress function in Saccharomyces cerevisiae. Microproteins with unique peptides were identified under six culture conditions: normal, oxidation, starvation, UV radiation, heat shock, and heat shock with starvation.
2022-06-07 | PXD028623 |
Project description:Stress events have transgenerational effects that influence plant growth in the subsequent generation. In Mediterranean regions, water-deficit and heat (WH) stress is a frequent issue that negatively affects crop yield and quality. Nitrogen (N) is an essential plant macronutrient and often a yield-limiting factor for crops. Here, the response of durum wheat seedlings to N starvation under the transgenerational effects of WH stress were investigated in two genotypes. Both genotypes showed significant reduction in seedling height, leaf number, shoot and root weight (fresh and dry), primary root length and chlorophyll content under N starvation stress. However, in the WH stress-tolerant genotype, the reduction rate of most traits were lower in progeny from the stressed parents than progeny from the control parents. Small RNA sequencing identified 1,534 microRNAs in different treatment groups. Differentially expressed microRNAs (DEMs) were characterized subject to N starvation, parental stress and genotype factors, with their target genes identified in silico. GO and KEGG enrichment analyses revealed the biological functions associated with DEM-target modules in stress adaptation processes, which could contribute to the phenotypic differences observed in two genotypes. The study provides the first evidence of the transgenerational effects of WH stress on N starvation response in durum wheat.
2021-04-21 | GSE168094 | GEO