Ontology highlight
ABSTRACT:
PROVIDER: PRJNA936930 | ENA |
REPOSITORIES: ENA
Dataset's files
| Action | DRS | |||
|---|---|---|---|---|
| SRR23587958_1.fastq.gz | Fastqsanger.gz | |||
| SRR23587958_2.fastq.gz | Fastqsanger.gz | |||
| SRR23587959_1.fastq.gz | Fastqsanger.gz | |||
| SRR23587959_2.fastq.gz | Fastqsanger.gz | |||
| SRR23587960_1.fastq.gz | Fastqsanger.gz |
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Project description:Despite the importance of amino acids as basic components of proteins, amino acids also serve as substrates for multiple other metabolic pathways, such as the TCA cycle that regulates energy homeostasis. The response to deficiency in the biosynthesis of specific amino acids (also termed âamino acid starvationâ) has been studied extensively in yeast (See for example Petti et. al., 2011 Survival of starving yeast is correlated with oxidative stress response and non-respiratory mitochondria function. Proc. Natl. Acad. Sci. USA 108: 1089-1098). In contrast, very little is known about the metabolic responses to deficiency in the biosynthesis of amino acids in plants. A number of recent reports have already shown that catabolism of amino acids can significantly contribute to cellular energy homeostasis particularly during the nighttime and particularly in response to stress. In the present manuscript we used a previously characterized Arabidopsis mutant with reduced expression of the Lys biosynthesis enzyme L,L-diaminopimelate aminotransferase (dapat) to investigate the physiological and metabolic impacts of deficient Lys biosynthesis. The results obtained demonstrate that not stomatal limitations but rather biochemical alterations are responsible for the decreased photosynthesis and growth of the dapat mutants which mimic stress conditions associated to Lys deficiency. Our findings suggest that manipulation of Lys biosynthesis in dapat mutant simulates a stress response culminating in a highly exquisite metabolic reprogramming such that alternative substrates support energy generation once carbohydrate metabolism is down-regulated.
2017-01-02 | E-MTAB-5315 | biostudies-arrayexpress
Project description:Mammalian preimplantation development is associated with marked metabolic robustness, and embryos can develop under a wide variety of nutrient conditions, including even the complete absence of soluble amino acids. Here we show that mouse embryonic stem cells (ESCs) capture the unique metabolic state of preimplantation embryos and proliferate in the absence of several essential amino acids. Amino acid independence is enabled by constitutive uptake of exogenous protein through macropinocytosis, alongside a robust lysosomal digestive system. Following transition to more committed states, ESCs reduce digestion of extracellular protein and instead become reliant on exogenous amino acids. Accordingly, amino acid withdrawal selects for ESCs that mimic the preimplantation epiblast. More broadly, we find that all lineages of preimplantation blastocysts exhibit constitutive macropinocytic protein uptake and digestion. Taken together, these results highlight exogenous protein uptake and digestion as an intrinsic feature of preimplantation development and provide insight into the catabolic strategies that enable embryos to sustain viability before implantation.
2023-09-22 | GSE234802 | GEO
Project description:Anaerobic microbial community enriched with amino acids
| PRJDB7737 | ENA
Project description:Metagenomic sequencing of anaerobic amino acids enrichments
| PRJNA598848 | ENA
Project description:Besides being building blocks for protein synthesis, amino acids serve a wide variety of cellular functions, including acting as metabolic intermediates for ATP generation and for redox homeostasis. Upon amino acid deprivation, free uncharged tRNAs trigger GCN2-ATF4 to mediate the well-characterized transcriptional amino acid response (AAR). However, it is not clear whether the deprivation of different individual amino acids triggers identical or distinct AARs. Here, we characterized the global transcriptional response upon deprivation of one amino acid at a time. With the exception of glycine, which was not required for the proliferation of MCF7 cells, we found that the deprivation of most amino acids triggered a shared transcriptional response that included the activation of ATF4, p53 and TXNIP. However, there was also significant heterogeneity among different individual AARs. The most dramatic transcriptional response was triggered by methionine deprivation, which activated an extensive and unique response in different cell types. We uncovered that the specific methionine-deprived transcriptional response required creatine biosynthesis. This dependency on creatine biosynthesis was caused by the consumption of S-Adenosyl-L-methionine (SAM) during creatine biosynthesis that helps to deplete SAM under methionine deprivation and reduces histone methylations. As such, the simultaneous deprivation of methionine and sources of creatine biosynthesis (either arginine or glycine) abolished the reduction of histone methylation and the methionine-specific transcriptional response. Arginine-derived ornithine was also required for the complete induction of the methionine-deprived specific gene response. Collectively, our data identify a previously unknown set of heterogeneous amino acid responses and reveal a distinct methionine-deprived transcriptional response that results from the crosstalk of arginine, glycine and methionine metabolism via arginine/glycine-dependent creatine biosynthesis. RNA was extracted by RNAeasy kits (Qiagen) from the MCF7 or PC3 cells which exposed to the control full DMEM or deprived one (or all) amino acid media for 24 or 48 hours.
2015-04-01 | E-GEOD-62673 | biostudies-arrayexpress
Project description:Cells constantly adapt to changes in their environment. In the majority of cases, the environment shifts between conditions that were previously encountered during the course of evolution, thus enabling evolutionary-programmed responses. In rare cases, however, cells may encounter a new environment to which a novel response is required. To characterize the first steps in adaptation to a novel condition, we studied budding yeast growth on xylulose, a sugar that is very rarely found in the wild. We previously reported that growth on xylulose induces the expression of amino-acid biosynthesis genes, in multiple natural yeast isolates. This induction occurs despite the presence of amino acids in the growth medium and is a unique response to xylulose, not triggered by any of the naturally available carbon sources tested. Propagating these strains for ~300 generations on xylulose significantly improved their growth rate. Notably, the most significant change in gene expression was the loss of amino acid biosynthesis gene induction. Furthermore, the reduction in amino-acid biosynthesis gene expression on xylulose was strongly correlated with the improvement in growth rate, suggesting that internal depletion of amino-acids presented the major bottleneck limiting growth in xylulose. We discuss the possible implications of our results for explaining how cells maintain the balance between supply and demand of amino acids during growth in evolutionary âfamiliarâ vs. ânovelâ conditions. mRNA profiles of 12 wt S. cerevisiae strains grown on either YPD or YP-xylulose, before and after 300 generations evolution on YP-xylulose
2015-12-17 | E-GEOD-76077 | biostudies-arrayexpress