Transcriptome profiles in E. coli under a prolonged starvation environment
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PROVIDER: PRJNA627713 | ENA |
REPOSITORIES: ENA
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Project description:How microorganisms resist nutrient-deficiency is important for understanding the pervasive prosperity of microbes in severe nutrient conditions. In laboratory culture, E. coli can survive for a long period of time under starvation, denoted as long-term stationary phase (LSP). Although physiology of those viable cells is of great interest, their genome-wide response has not yet been fully understood. In this study, we employed high-density oligonucleotide array to investigate the transcriptional profile of the cells exposed with supernatant of LSP culture. We compared the expression profiles of LSP to those of exponentially and short-term stationary phase, and revealed that the cellular physiology in the LSP environment is primarily represented by up-regulation of transporter genes and down-regulation of biosynthesis genes, which is similar to those in the short-term stationary phase. Our analysis further detected the differentially expressed functional gene categories between short- and long-term stationary phase, in terms of increasing the expressions of some stress-response genes and repressing the translational genes expressions, suggesting more survival/maintenance weighted metabolism in LSP. We also found the population-density-susceptible expression profiles in the LSP condition, which is also informative to understand the survival mechanism in long-term starvation.
2020-04-24 | GSE149236 | GEO
Project description:p53-specific transcriptome under starvation
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Project description:Nutrient intake is tightly linked to animal energy metabolism and growth. Inhibition of anabolic processes during nutrient deprivation is a critical stress response necessary for survival. However, how transient vs. prolonged nutrient deprivation is sensed by the key metabolic organs and which downstream pathways mediate metabolic regulation under these conditions remain insufficiently understood. Here we uncover an unexpected role for the transcription factor Spalt-related (Salr), a known to be involved in wing morphogenesis, as a regulator of growth and metabolism upon nutrient starvation. Specifically, we observed that Salr is necessary and sufficient to inhibit cellular and organismal growth as well as lipid storage in the Drosophila fat body. Our results indicate that Salr inhibits anabolic processes through the regulation of mTOR complex 1 activity as well as by directly controlling genes involved in lipid catabolism and autophagy. We discovered that Salr and FoxO, a known downstream target of insulin signalling, act on overlapping set of target genes, but are regulated in a sequential manner. While FoxO is activated transiently upon starvation, Salr displays delayed activation kinetics. In conclusion, our results reveal a novel starvation-activated catabolic switch in the fat body, which is closely interconnected with the insulin/mTOR pathway.
2026-06-23 | GSE305957 | GEO
Project description:Spalt-related is a catabolic switch activated by prolonged starvation
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Project description:Comparison of gene expression for Chlamydomonas cells grown for 24h, 48h, 72h, 96h under nitrogen starvation
2011-10-19 | GSE33041 | GEO
Project description:Sugar is an important resource for energy generation and developmental regulation in plants, and sucrose starvation causes enormous changes in cellular morphology, enzyme activities and gene expression. Genome-wide gene expression profiling provides a comprehensive knowledge into gene expression under nutrients depletion and senescence, however, that of monocot model plant rice under sucrose depletion is still under investigation. Here, the time-course monitoring of gene expression profiles in sucrose-starved rice (Oryza sativa cv Tainung67) suspension cells was investigated by 21495 probes-containing Agilent rice chip. In sucrose-starved cells, the induced vacuolar biogenesis was coincided with the significantly upregulated expression of genes encoding H+-pyrophosphatase, delta-TIP, one putative alpha-TIP, several vacuolar proteases and proteinase inhibitors, and one OsATG3. To survey the overall metabolic adaptations under sucrose depletion the genes significantly alternating expression level were incorporated into multiple metabolic pathways. The majority of genes encoding enzymes involved in biosynthesis and degradation pathways of various macromolecules were comprehensively down- and upregulated, respectively, by sucrose starvation. Transcriptional regulation of gene expression is important for the physiological adaptations to environmental stress and many transcription factors, including bZIPs, NACs, and WRKY showed significant increase in transcript levels under sucrose starvation. Concurrently, statistical analysis reveals that their corresponding consensus cis-elements, such as ABA-responsive element, CACG, ACI, ACII and CTTATCC, are frequently found in the promoter regions of many Suc starvation-upregulated genes. Particle bombardment-mediated transient promoter activity assays further showed that the CTTATCC, derived form TATCCA, and the AC motifs, are the promising sucrose starvation responsive activators in sucrose-starved rice suspension cells. Keywords: stress response
2006-09-20 | GSE5853 | GEO
Project description:To investigate mechanism of inosine promotes the survival and metabolism of MDA-MB-231 cells under starvation conditions, MDA-MB-231 cells were treated with inosine and glucose for 12h under starvation conditions. We then performed gene expression profiling analysis using data obtained from RNA-seq of MDA-MB-231 cells under three different treatments（-G-Q,Inosine,Glucose）.
2023-07-17 | GSE225643 | GEO
Project description:Circadian clocks are evolved to adapt to the daily environment changes under different conditions. The ability to maintain circadian clock functions in response to various stress and perturbations is important for organismal fitness. Here, we show that the nutrient sensing GCN2 signaling pathway is required for robust circadian clock function under amino acid starvation in Neurospora. The deletion of GCN2 pathway components disrupts rhythmic transcription of clock gene frq by suppressing WC complex binding at the frq promoter due to its reduced histone H3 acetylation levels. Under amino acid starvation, the activation of GCN2 kinase and its downstream transcription factor CPC-1 establish a proper chromatin state at the frq promoter by recruiting the histone acetyltransferase GCN-5. The arrhythmic phenotype of the GCN2 kinase mutants under amino acid starvation can be rescued by inhibiting histone deacetylation. Finally, genome-wide transcriptional analysis indicates that the GCN2 signaling pathway maintains robust rhythmic expression of metabolic genes under amino acid starvation. Together, these results uncover an essential role of GCN2 signaling pathway in maintaining robust circadian clock function in response to amino acid starvation and the importance of histone acetylation at the frq locus in rhythmic gene expression.
2023-05-08 | GSE220169 | GEO
Project description:Marron (Cherax cainii) gut metagenome under starvation Metagenome
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Project description:We performed a transcriptomic analysis of Pi starvation responses in Arabidopsis thaliana (Columbia-0) wild type plants under phosphate starvation stress and in plants with altered PHR1(-like) activity, comparing mutants of phr1 and phr1-phl1 grown in phosphate-lacking medium. Results show the central role of PHR1 and functionally redundant members of its family in the control of transcriptional responses to Pi starvation.
2010-12-09 | GSE16722 | GEO