E-GEOD-99576
Ontology highlight
ABSTRACT:
PROVIDER: E-GEOD-99576 | ExpressionAtlas | 2020-04-14
REPOSITORIES: ExpressionAtlas
Dataset's files
| Action | DRS | |||
|---|---|---|---|---|
| E-GEOD-99576-analysis-methods.tsv | Tabular | |||
| E-GEOD-99576-analytics.tsv | Tabular | |||
| E-GEOD-99576-atlasExperimentSummary.Rdata | Rdata | |||
| E-GEOD-99576-configuration.xml | Xml | |||
| E-GEOD-99576-g1_g4-mvaPlot.png | Other |
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Project description:Exploring the link between ER stress and autophagy in Arabidopsis
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Project description:UFMylation mediates the covalent modification of substrate proteins with UFM1 (Ubiquitin- fold modifier 1) and regulates the selective degradation of endoplasmic reticulum (ER) via autophagy (ER-phagy) to maintain ER homeostasis. Specifically, collisions of the ER-bound ribosomes trigger ribosome UFMylation, which in turn activates C53-mediated autophagy that clears the toxic incomplete polypeptides. C53 has evolved non-canonical shuffled ATG8 interacting motifs (sAIMs) that are essential for ATG8 interaction and autophagy initiation. Why these non-canonical motifs were selected during evolution, instead of canonical ATG8 interacting motifs remains unknown. Here, using a phylogenomics approach, we show that UFMylation is conserved across the eukaryotes and secondarily lost in fungi and some other species. Further biochemical assays have confirmed those results and showed that the unicellular algae, Chlamydomonas reinhardtii has a functional UFMylation machinery, overturning the assumption that this process is linked to multicellularity. Our conservation analysis also revealed that UFM1 co-evolves with the sAIMs in C53, reflecting a functional link between UFM1 and the sAIMs. Using biochemical and structural approaches, we confirmed the interaction of UFM1 with the C53 sAIMs and found that UFM1 and ATG8 bound to the sAIMs in a different mode. Conversion of sAIMs into canonical AIMs prevented binding of UFM1 to C53, while strengthening ATG8 interaction. This led to the autoactivation of the C53 pathway and sensitized Arabidopsis thaliana to ER stress. Altogether, our findings reveal an ancestral toggle switch embodied in the sAIMs that regulates C53- mediated autophagy to maintain ER homeostasis.
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Project description:Autophagy is a conserved process in eukaryotes that contributes to cell survival in response to stress. Previously, we found that ER stress induces autophagy in a manner dependent upon IRE1b, an ER membrane-associated factor involved in the splicing of bZIP60 mRNA. IRE1 is a dual protein kinase and ribonuclease, and here we studied the involvement of the protein kinase catalytic domain, nucleotide binding and RNase domains of IRE1b in activating autophagy. Autophagy was assessed by quantifying the numbers of autophagosomes in transgenic Arabidopsis seedlings bearing mutations in the various IRE1b domains. The results showed that nucleotide binding and RNase activity of IRE1b are required for ER stress-mediated autophagy. The RNase activity is involved in IRE1b’s mRNA splicing function, but its principal splicing target, bZIP60, is not involved in IRE1b’s activation of autophagy. We therefore considered other roles for IRE1b in the activation of autophagy. Clustering of ER localized IRE1b-YFP was observed when seedlings were subjected to ER stress, and so we investigated whether IRE1b clustering induced autophagy. However, the RNase knockout mutation in IRE1b still undergoes clustering, suggesting that IRE1b clustering does not induce autophagy. In response to ER stress, the RNase of IRE1 has been found to engage in another activity called Regulated Ire1-Dependent Decay of Messenger RNA (RIDD), which is the promiscuous degradation of other mRNA in response to ER stress. By analyzing the RNA-seq data, 12 RIDD target genes were picked up for testing their role in inhibiting autophagy, and glucosidase 21 and peroxidase 14 are proved to be degraded to support the induction of autophagy by ER stress.
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Project description:We have identified a potential selective autophagy receptor protein in Arabidopsis thaliana, C53/AT5G06830/ERP1, that is recruited to ER upon ER-stress activation and induces autophagosome formation. By affinity proteomics IP/MS with ATG8A and E, we identified this new ER-phagy receptor, which is also conserved in metazoans. With biophysical characterization, we revealed its unprecedent binding mode to ATG8 (sAIM). C53 senses proteotoxic stress in the ER lumen by forming a tripartite receptor complex with the ER-associated ufmylation ligase UFL1 and its membrane adaptor DDRGK1. However, its cargo targeted for degradation is still elusive. Initial quantitative proteomics analyses (TMT) of wild type and Atc53 mutant lines revealed that Atc53 mediates degradation of ER resident proteins as well as proteins passaging the ER to the cell wall, apoplast, and lipid droplets.
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Project description:A comparative analysis between wild-type Arabidopsis thaliana and autophagy´s atg5 mutant to discover differences between these two plants during normal growth and in relationship to water deficit
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Project description:We have implemented an integrated Systems Biology approach to analyze overall transcriptomic reprogramming and systems level defense responses in the model plant Arabidopsis thaliana during an insect (Brevicoryne brassicae) and a bacterial (Pseudomonas syringae pv. tomato strain DC3000) attack. The main aim of this study was to identify the attacker-specific and general defense response signatures in the model plant Arabidopsis thaliana while attacked by phloem feeding aphids or pathogenic bacteria. Defense responses and networks, unique and specific for aphid or Pseudomonas stresses were identified. Our analysis revealed a probable link between biotic stress and microRNAs in Arabidopsis and thus opened up a new direction to conduct large-scale targeted experiments to explore detailed regulatory links among them. The presented results provide a first comprehensive understanding of Arabidopsis - B. brassicae and Arabidopsis - P. syringae interactions at a systems biology level.
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Project description:These ChIP-seq data files are part of a study where a comparison was made between the change in transcription and H3K4 mono-, di-, and tri-methylation levels in the Arabidopsis thaliana genome when plants are subjected to water deficit stress. Keywords: stress response, histone modification
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Project description:Comprehensive understanding of the transcriptional foundations of human intestinal ischemia-reperfusion (IR) injury is imperative to find therapeutic targets and improve patient outcome. Here we analysed transcriptomes of the IR-injured human intestine, and showed that over 1,800 genes were significantly differentially expressed, predominantly during reperfusion. Intriguingly, protein processing in endoplasmic reticulum (ER) was one of the most perturbed pathways, which was supported by ontology analysis. The IR-triggered transcriptome is organized into distinct co-expression networks, and implied a role for HIF1-alpha in the response towards unfolded proteins. Unfolded protein response activation as a consequence of ER stress was further validated in a large sample set, revealing strong correlations between expression of ER stress genes IRE1, XBP1 and BiP and autophagy gene LC3B. Moreover, signs of ER stress and autophagy, particularly ER phagy, were apparent in Paneth cells. Collectively, these findings provide new evidence for key involvement of protein folding stress in IR-induced intestinal injury in man. The ensuing ER stress, together with its manifestations in Paneth cells, likely contributes to IR-induced complications including bacterial penetration and inflammation.
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