GCN2 adapts the proteome to scavenging-dependent growth
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ABSTRACT:
PROVIDER: PRJNA634769 | ENA |
REPOSITORIES: ENA
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Project description:We report the transcriptional and translational changes that occur upon leucine deprivation +/- GCN2.
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Project description:When eukaryotic cells are deprived of amino acids, uncharged tRNAs accumulate and activate the conserved GCN2 protein kinase. We examine how yeast growth and tRNA charging or aminoacylation is affected during amino acid depletion in the presence and absence of GCN2. tRNA charging is measured using a microarray technique which allows for simultaneous measurement of all cytosolic tRNAs. A fully prototrophic and its isogenic GCN2 deletion strain were used. We measured relative tRNA charging levels in yeast strains with an intact and deleted GCN2.
2010-08-01 | E-GEOD-22452 | biostudies-arrayexpress
Project description:Protein synthesis is costly and the proteome size is constrained. Using a genome-scale computational model of proteome allocation together with absolute proteomics data sets from many growth environments, we determine how these fundamental limitations constrain growth and fitness in Escherichia coli. First, we show that the observed variation in growth rates across environments is largely determined by the expression of protein not utilized for growth in a given environment. We then elucidate the overall transcriptional regulatory logic that underlies the expression of unused protein. We systematically classify the unused proteome into segments devoted to environmental readiness and stress resistance functions. While expression of these proteome segments incurs a fitness cost of decreased growth in a fixed environment, they provide fitness benefits in a changing environment. Thus, the systems biology of the prokaryotic proteome can be quantitatively understood based on resource allocation to growth, environmental readiness, and stress resistance functions.
2018-08-01 | GSE72020 | GEO
Project description:When eukaryotic cells are deprived of amino acids, uncharged tRNAs accumulate and activate the conserved GCN2 protein kinase. We examine how yeast growth and tRNA charging or aminoacylation is affected during amino acid depletion in the presence and absence of GCN2. tRNA charging is measured using a microarray technique which allows for simultaneous measurement of all cytosolic tRNAs. A fully prototrophic and its isogenic GCN2 deletion strain were used.
2010-08-01 | GSE22452 | GEO
Project description:General control nonderepressible 2 (GCN2) phosphorylates eIF2α, regulating translation in response to nutritional stress. Here, we show that mammalian ribosomes are potent GCN2 activators. Hydrogen/deuterium exchange–mass spectrometry (HDX-MS) showed GCN2 interacting with domain II of the uL10 P-stalk protein. The P-stalk is a uL10/P12/P22 pentameric complex that is part of the ribosomal GTPase-associated center. Recombinant human P-stalk greatly stimulates GCN2. Both domain II of uL10 and the C-terminal tails of P1 and P2 are necessary for maximal GCN2 activation. On actively translating ribosomes, the C-terminal tails of P1 and P2 are sequestered by elongation factors, suggesting P-stalk availability could link translational stress to GCN2 activation.
2019-05-24 | PXD013051 | Pride
Project description:Non-shivering thermogenesis in the brown adipose tissue (BAT) of rodents requires macronutrients to fuel the generation of heat during hypothermic conditions. Therefore, it is critical to identify signaling pathways which aid in nutrient delivery within this thermogenic tissue.To understand the contribution of the integrated stress response (ISR) in directing adaptive thermogenesis, we examined the role of the kinase activity of general control nonderepressible 2 (GCN2) within the BAT during acute cold exposure. We hypothesized that under hypothermic conditions, GCN2 maintains thermogenesis via ISR gene targets such as fibroblast growth factor 21 (FGF21), that triggers thermogenic uncoupling in BAT. In alignment with our hypothesis, both female and male mice either lacking GCN2 or administered a small molecule inhibitor of GCN2 were profoundly intolerant to acute cold stress. However, while GCN2 deletion in male mice impeded liver-derived FGF21 expression, it did not affect FGF21 levels in females, suggesting an alternative role for GCN2 in the maintenance of thermogenesis. Within the BAT, acute cold exposure increased ISR target genes and thermogenic genes regardless of GCN2 status and sex. RNA sequencing in BAT during cold exposure revealed a gene signature that identified actomyosin mechanics and transmembrane transport as the top two processes requiring GCN2. The top gene signature included cytoskeletal and class II myosin heavy chain genes critical for maximal thermogenesis during cold stress. The second gene signature included amino acid transporters which corresponded with higher circulating amino acids. In conclusion, we identify a novel role for GCN2 activation during acute cold exposure to facilitate mechanosensitive cell signaling and use of amino acids for adaptive thermogenesis.
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Project description:In response to different cellular stressors, the ISR kinases, PERK, PKR, HRI and GCN2, activate downstream transcriptional programs. While the core ISR transcription program is well characterized, markers that are specific to each individual ISR kinase activation pathway are not known. To identify markers that are induced by PERK or GCN2, but not the other ISR kinases, we subjected WT, GCN2-/-, and PERK-/- MEFs to amino acid starvation (RPMI 1640 SILAC -Lys -Arg) or Thapsigargin (200nM) treatment for 6 hours to activate the GCN2 and PERK pathways, respectively and performed RNA sequencing.
2022-07-01 | GSE179559 | GEO
Project description:Diverse environmental insults induce the integrated stress response (ISR), which features eIF2 phosphorylation and translational control that serves to restore protein homeostasis. The eIF2 kinase GCN2 is a first responder in the ISR that is activated by amino acid depletion and other unrelated stresses. Two processes are suggested to trigger an ordered process of GCN2 activation during stress: GCN2 monitoring stress via accumulating uncharged tRNAs or by stalled and colliding ribosomes. Our results suggest that while ribosomal collisions are indeed essential for GCN2 activation in response to translational elongation inhibitors, conditions that trigger deacylation of tRNAs activate GCN2 via its direct association with affected tRNAs. Both process require the GCN2 regulatory domain related to histidyl tRNA synthetases. GCN2 activation by UV irradiation features lowered amino acids and increased uncharged tRNAs and ribosome collisions are dispensable. We conclude that there are multiple mechanisms that activate GCN2 during diverse stresses.
2024-03-06 | GSE239867 | GEO