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:It is the study to investigate the growth and transcriptome of Arabidopsis thaliana exposed to submergence or flooding with physical flow.
Project description:This study profiles transcriptomic changes of Arabidopsis thaliana Col-0 in response to submergence. This dataset includes CEL files, RMA signal values and MAS5 P/M/A calls from total mRNA populations of plants at 9 to 10 leaf rosette stage. Biological replicates of root and shoot tissues were harvested after 7 h and 24 h of submergence in darkness along with corresponding non-submerged dark controls. To characterize the dark response, non-submerged light controls plants were harvested at the 0 h time point. Quantitative profiling of cellular mRNAs was accomplished with the Affymetrix ATH1 platform. Changes in the transcriptome in response to submergence and early darkness were evaluated, and the data led to identification of genes co-regulated at the conditional and organ-specific level.
Project description:While the molecular mechanisms mediating submergence tolerance have been extensively studied, those underpinning age-dependent resilience remain poorly characterized. In Arabidopsis thaliana, submergence elicits a leaf-age dependent phenotype in which senescence and death progress across an age gradient starting with older leaves. Here we sought to investigate the mechanisms mediating this observed differential flood resilience by interrogating leaf age-specific transcriptome and proteome changes during submergence and recovery. Following submergence, most age-dependent differences were in the magnitude or speed of transcript abundance changes, whereas qualitative leaf-age dependent responses were most apparent during recovery. This included a strong desiccation response in old leaves despite a stronger ABA-signaling response. Physiological measurements suggested that faster dehydration was mediated by a combination of submergence-mediated reduction of ABA sensitivity and higher conductance in old leaves. We also observed a stronger induction in young shoot tissue of genes associated with endoplasmic reticulum (ER) stress and the unfolded protein response (UPR). Mutants disabled in the two UPR signaling branches were affected in new leaf formation and the ability to restore the proteome, but not in senescence, suggesting that young tissues activate ER stress recovery to permit continuation of growth. Of the mitochondrial membrane proteins differentially regulated in young leaves, loss of mitochondrial voltage-dependent anion channel function impacted submergence-recovery tolerance. Our data reveal multiple mechanisms underlying leaf age-dependent differential submergence recovery and demonstrate how tolerance is determined by an interplay between age related developmental traits and stress signaling pathways.
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
Project description:Kinetic model of extended MEP pathway in Arabidopsis thaliana for isoprene.
This model was used for determining total optimization potential (TOP) of isoprene production in Arabidopsis thaliana using Spacescanner (https://github.com/atiselsts/spacescanner). This model was used to make designs D, E and F. An optimization task in COPASI can be perfomed using this model by accesing COPASI/Tasks/Optimization. Parameters which will be changed during the optimization and the optimization constraints can be selected.
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Total optimization potential (TOP) approach based constrained design of isoprene and cis-abienol production in A. thaliana,
Authors: Katrina D. Neiburga, Reinis Muiznieks, Darta M. Zake, Agris Pentjuss, Vitalijs Komasilovs, Johann Rohwer, Alain Tissier, Egils Stalidzans
