Project description:We analyzed global transcriptional changes in submerged Arabidopsis seedlings comparing control untreated seedlings. The same analysis were also applied on wrky22-ko2 seedling to identify WRKY22 targets under submergence.
Project description:Arabidopsis plants display superior tolerance to submergence at the juvenile stage. We characterized the transcriptomic response to submergence in juvenile and adult plants. In this dataset, we include expression data from 2-week and 3-week old plants under dark air and dark submergence conditions.
Project description:Arabidopsis, at the 10 leaf stage, was given kept under control growth conditions, complete darkness, or complete darkness together with complete submergence for 4 hours. These treatments were given to eight accession varying in tolerance to complete submergence, namely Cvi-0, Bay-0, Ita-0, Col(gl), Kas-1, Lp2-6, Ws-2, C24. Additionally, both roots or entire shoots were harvested. Overall this allowed the identification of conserved responses to darkness and submergence in addition to variation in the transcriptomic response potentially related to tolerance to complete submergence. An additional layer of post transcriptional regulation (alternative splicing) was also uncovered by this data.
Project description:General translational repression is predicted as a key process to reduce energy consumption under hypoxia. We have previously showed that mRNA loading onto polysome is reduced in Arabidopsis under submergence. Here, we showed that plant stress activated GCN2 (general control nonderepressible 2) can phosphorylate eIF2a (Eukaryotic Initiation Factor 2a) in Arabidopsis under submergence, and this process is reversible after desubmergence. Compared to the wild-type, the reduction in polysome loading during submergence was less severe in the gcn2 mutant. Transgenic lines overexpressing GCN2 had more ATP and conferred better tolerance under submergence, suggesting that GCN2 might modulate the dynamics of translation to adjust the energy homeostasis under hypoxia. Interestingly, GCN2-eIF2a signaling was activated by ethylene under submergence. However, GCN2 activity was not affected in ein2-5 and eil1ein3 under submergence, suggesting that GCN2 activity was regulated by noncanonical ethylene signaling. In addition, the polysome loading was retained in both ein2-5 and etr1-1 under submergence, implying that ethylene modulated the dynamic translation under submergence via EIN2 and GCN2. Notably, our NGS analysis also demonstrated that EIN2 and GCN2 regulated the translation of 23 core hypoxia genes as well as 53% translational repressed genes under submergence. On the other hand, EIN2 and GCN2 also affected the expression of genes involved in hypoxic response, ethylene response, biotic stress and negative regulation of cytokinin signaling. Taken together, these demonstrated that entrapped ethylene triggers GCN2 and EIN2 to ensure the translation of stress required proteins under submergence and also provide a step stone for future investigation how eukaryotic cells modulate the translation to response for the changeable environments.
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.
Project description:The goal of this study is to compare translation regulation in Col-0, SnRK1, and eIFiso4G1 mutants in Arabidopsis under submergence
