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ABSTRACT:
PROVIDER: PRJNA769614 | ENA |
REPOSITORIES: ENA
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Project description:Autophagy is an essential cellular process in eukaryotes that degrades and recycles macromolecules and organelles. Defects in autophagy is known to affect metabolism, including the lipidome. Genetic approaches have identified a series of AuTophaGy-related (ATG) genes in Arabidopsis. In this study we used WT (ecotype Col-0) and two Arabidopsis autophagy-defective mutants, atg7 and atg9 to perform a multi-omics study on the effect of nitrogen starvation treatment, which induces autophagy. Specifically, we have quantified ~100 lipids from leaf and root tissues of WT, atg7 and atg9 mutant plants, under either autophagy-inducing conditions (-N) or normal nitrogen conditions (+N). The lipid species we quantified include: DGDG, MGDG, LPC, LPE, PE, LPG, PC, PA, PG, PI, and PS. Our study sheds lights on the understanding of the relationships between autophagy and metabolism, especially lipid metabolism.
2022-02-21 | ST002252 | MetabolomicsWorkbench
Project description:Autophagy as a conserved degradation and recycling machinery is important in normal development and physiology, and defects in this process are linked to many kinds of disease. Because too much or too little autophagy can be detrimental, the process must be tightly regulated both temporally and in magnitude. The transcriptional induction and repression of the autophagy-related (ATG) genes is one crucial aspect of this regulation, but the transcriptional regulators that modulate autophagy are not well characterized. In this study, we identified Pho23 as a master transcriptional repressor for autophagy, with transcriptome profiling revealing that ATG9 is one of the key target genes. Physiological studies with a PHO23 null mutant, or with strains expressing modulated levels of Atg9, demonstrate a critical role of this protein as a regulator of autophagosome formation frequency; Atg9 protein levels correlate with the number of autophagosomes generated upon autophagy induction, and the level of autophagy activity. WT yeast and pho23 deletion mutants were grown under nutrient rich or nitrogen starvation conditions; gene expression was quantified across these 4 samples.
2014-04-24 | E-GEOD-57031 | biostudies-arrayexpress
Project description:In Saccharomyces cerevisiae, Atg9 is an important AuTophaGy-related (Atg) protein, plays critical roles in regulating macroautophagy/autophagy, and physically interacts with hundreds of proteins. How Atg9 interacting partners are synergistically orchestrated in autophagy are unclear. Here, we conducted a transcriptomic and proteomic profiling of Atg9-dependent molecular landscapes during nitrogen starvation-induced autophagy.
2019-01-19 | PXD012458 | iProX
Project description:As a core Autophagy-related (Atg) protein during yeast autophagy, Atg1 interacts with numerous other proteins, and its kinase activity facilitates to phosphorylate various substrates. How Atg1-interacting partners and substrates synergistically orchestrate autophagy remains to be further dissected. In this study, we conducted a transcriptomic, proteomic and phosphoproteomic profiling of Atg1-dependent molecular landscapes during nitrogen starvation-triggered autophagy.
2021-12-23 | PXD030628 | iProX
Project description:Autophagy involves massive degradation of intracellular components and functions as a conserved system that helps cells to adapt to adverse conditions. In Arabidopsis thaliana, submergence induces the transcription of autophagy-related (ATG) genes and the formation of autophagosomes. To study the role of autophagy during submergence, we performed transcriptome analysis with atg5, an autophagy-defective mutant, under submergence conditions. Our data showed that submergence changed the expression profile of DEG in the atg5 versus wild-type.
2021-09-20 | GSE184340 | GEO
Project description:Transcription factor EB (TFEB), well characterized as a master regulator of autophagy and lysosomal biogenesis, is translocated to the nucleus and activated by varieties of cellular stresses including starvation and lysosomal damage. However, compared to the starvation condition, the molecular mechanism of TFEB activation by other stress conditions is poorly understood. Previously, we have shown that TFEB activation during lysosomal damage but not starvation condition depends on a subset of autophagy regulators, collectively called ATG conjugation system, whose function is essential for the lipidation of ATG8 proteins. In this study, by time-lapse imaging, we newly identified the presence of ATG conjugation system -independent TFEB regulation which precedes the ATG conjugation system-dependent regulation, designated mode I and mode II, respectively. Consistent with the presence of different modes, our time course transcriptome analysis revealed two different sets of TFEB downstream. Comprehensive interactome analysis of TFEB and subsequent functional screening identified unique regulars of TFEB in each mode: APEX1 for Mode I and CCT7 and/or TRIP6 for Mode II, respectively. APEX1 interacted with TFEB and was required for its protein stability in a manner independent of ATG conjugation system. On the other hand, both CCT7 and TRIP6 were accumulated on lysosomes during lysosomal damage and interacted with TFEB mainly in ATG conjugation system deficient cells, presumably blocking TFEB nuclear translocation. Moreover, we further revealed that TFEB regulatory mechanisms by other cellular stresses such as oxidative stress, proteasome inhibition, mitochondria depolarization, and DNA damage can be classified into either APEX1-mediated Mode I or TRIP6-mediated Mode II. Our results pave the way for a unified understanding TFEB regulatory mechanisms from the perspective of ATG conjugation system under varieties of cellular stresses.
2024-03-31 | GSE235340 | GEO
Project description:Autophagy is a eukaryotic bulk degradation pathway that allows cells to degrade potentially harmful cytosolic components or to provide necessary nutrients during starvation. This cargo degradation is achieved by its sequestration within double membrane vesicles termed autophagosomes, which fuse with the vacuole where it is degraded. Atg (autophagy-related) proteins are the main group of proteins involved in this process and, interestingly, Atg9 is the only integral membrane yeast Atg protein absolutely required for autophagy progression. In the cell it resides in Golgi-derived vesicles, which are indispensable for the nucleation of the autophagosome. There is not much known about biochemical properties of these vesicles in particular their protein content apart from Atg9. To address this question and to identify putative interaction partners of Atg9, the Atg9-vesicles were isolated and submitted to mass spectrometry analysis.
2022-03-03 | PXD020359 | Pride
Project description:The energy sensor AMP-activated protein kinase (AMPK) can activate autophagy when cellular energy production becomes compromised. However, the degree to which nutrient sensing impinges on the autophagosome closure remains unknown. Here, we provide the mechanism underlying a plant unique protein FREE1, upon autophagy-induced SnRK1α1-mediated phosphorylation, functions as a linkage between ATG conjugation system and ESCRT machinery to regulate the autophagosome closure upon nutrient deprivation. Using high-resolution microscopy, 3D-electron tomography, and protease protection assay, we showed that unclosed autophagosomes accumulated in free1 mutants. Proteomic, cellular and biochemical analysis revealed the mechanistic connection between FREE1 and the ATG conjugation system/ESCRT-III complex in regulating autophagosome closure. Mass spectrometry analysis showed that the evolutionary conserved plant energy sensor SnRK1α1 phosphorylates FREE1 and recruits it to the autophagosomes to promote closure. Mutagenesis of the phosphorylation site on FREE1 caused the autophagosome closure failure. Our findings unveil how cellular energy sensing pathways regulate autophagosome closure to maintain cellular homeostasis.
2023-03-30 | PXD040435 | Pride
Project description:Autophagy is a conserved process that recycles cellular contents to promote survival. Although nitrogen starvation is the canonical inducer of autophagy, recent studies have revealed several other nutrients important to this process. In this study, we used a quantitative, high-throughput assay to identify potassium starvation as a new and potent inducer of autophagy. We found that potassium-dependent autophagy requires the core pathway kinases Atg1, Atg5, Vps34, as well as other components of Phosphatidylinositol 3-kinase Complex I. Transmission electron microscopy revealed abundant autophagosome formation in response to both stimuli. RNA sequencing indicated distinct transcriptional responses – nitrogen affects transport of ions such as copper while potassium targets the organization of other cellular components. Thus, nitrogen and potassium share the ability to influence metabolic supply and demand but do so in different ways. Both inputs promote catabolism through bulk autophagy, but inhibit cellular anabolism through distinct mechanisms.
2020-06-06 | GSE151898 | GEO
Project description:We report global gene expression profilies of Brassinosteroid related Arabidopsis mutants in response to dehydration and fixed-carbon starvation stresses by RNA-seq
2017-04-11 | GSE93420 | GEO