Autotoxicity mechanism of Oryza Sativa: Microarray analysis of rice plants in response to allelochemical ferulic acid
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ABSTRACT:
ORGANISM(S): Oryza sativa
PROVIDER: GSE34899 | GEO | 2013/07/22
SECONDARY ACCESSION(S): PRJNA150185
REPOSITORIES: GEO
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Project description:Autotoxicity plays an important mechanism in regulating plant productivity. Ferulic acid (FA) is phytotoxic and was identified in extracts and residues of rice plants as a candidate for rice allelochemicals. To help characterize the autotoxicity mechanism of rice, we present the first large-scale, transcriptomic analysis of rice root responses to ferulic acid. Two-condition experiment, short exposures and long exposures. Comparison of mock control and rice seedlings treated with 50 ppm ferulic acid (FA) during short (pooled from 1- and 3-h treatments), as compared to long (24 h) exposures.; Biological replicates: 3 control replicates (short and long exposures), 3 FA-treated replicates (short and long exposures).
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Project description:Gene expression in N2 worms treated with 500 μM or 0 μM ferulic acid, at days 5. Effects of ferulic acid in C. elegans gene expression is studied, as our results indicate a lifespan extension effect produced by this molecule. RNA-seq were used to detail the global programme of gene expression underlying the lifespan extension and identified distinct classes of up/down-regulated genes in animals treated with ferulic acid.
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Project description:Corynebacterium glutamicum can survive by using ferulic acid as the sole carbon source. In this study, we assessed the response of C.glutamicum to ferulic acid stress by means of a global transcriptional response analysis. The transcriptional data showed that several genes involved in degradation of ferulic acid were affected. Moreover, several genes related to the stress response; protein protection or degradation and DNA repair; replication, transcription and translation; and the cell envelope were differentially expressed. Deletion of the katA or sigE gene in C. glutamicum resulted in a decrease in cell viability under ferulic acid stress. These insights will facilitate further engineering of model industrial strains, with enhanced tolerance to ferulic acid to enable easy production of biofuels from lignocellulose.
2017-09-01 | GSE86537 | GEO
Project description:The presence of anti-microbial phenolic compounds, such as the model compound ferulic acid, in biomass hydrolysates poses significant challenges to the widespread use of biomass in conjunction with whole cell biocatalysis or fermentation. Currently, these inhibitory compounds must be removed through additional downstream processing to create feedstock suitable for most industrially important microbial strains. This study explores the high ferulic acid tolerance in Lactobacillus brevis (L. brevis), a lactic acid bacteria often found in fermentation processes, by global transcriptional response analysis. The transcriptional profile of L. brevis under ferulic acid stress reveals that the presence of ferulic acid primarily triggers the expression of membrane proteins to counteract ferulic acid induced changes in membrane fluidity and ion leakage, in the midst of a generalized stress response. Several promising routes for understanding phenolic acid tolerance have been identified based upon these findings. These insights may be used to guide further engineering of model industrial organisms to better tolerate phenolic compounds in processed biomass. Three biological replicates were utilized for each time point. Total RNA was extracted using the Zymo Research Bacterial/Fungal RNA extraction kit Microarrays were indirectly labeled, hybridized, and washed according to the Fairplay III Kit protocol. Slides were scanned using the Axon GenePix 4200A scanner. Data normalization (LOWESS) was carried out on each array separately. The arithmetic average of probe signals was used to compute Log2 values.
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Project description:The impacts of ferulic acid, a phenolic compound commonly found in lignin hydrolysates, on the growth, solvent production and transcriptional responses of C. beijerinckii NCIMB 8052 were determined. Addition of ferulic acid to growing cultures resulted in a decrease in the growth and solvent production by 30 and 25%, respectively, when compared to the control cultures. To better understand the toxicity of this compound, microarray analyses were performed using samples taken from these cultures at three different growth states. Several gene ontology terms and KEGG pathways were identified showing significant change at each status, including ABC transporters, two component system and oxidoreductase activity. Moreover, genes related with efflux systems and heat shock proteins were also strongly up- regulated. Among these, expression of the groESL operon was induced by more than 4-fold and was consequently selected for overexpression to improve C. beijerinckii tolerance to ferulic acid.
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Project description:Juglone is phytotoxic and has been widely studied for allelopathic effects, but the molecular mode of action of allelochemicals is not well understood.To gain more insight into cellular responses to juglone, we have taken a large-scale analysis of the rice transcriptome during juglone stress. Exposure to juglone triggered changes in the transcript levels for several genes related to cell rescue and defense, with the majority of these genes potentially associated with chemical detoxification pathways, abiotic stress response pathway, cell wall formation and epigenetic mechanism. Molecular mechanisms for the allelochemical,juglone, in rice roots Comparison of mock control and rice seedlings treated with 10mM juglone; Biological replicates: 3 control replicates, 3 juglone-treated replicates.
2011-08-16 | E-GEOD-27413 | biostudies-arrayexpress
Project description:Juglone is phytotoxic and has been widely studied for allelopathic effects, but the molecular mode of action of allelochemicals is not well understood.To gain more insight into cellular responses to juglone, we have taken a large-scale analysis of the rice transcriptome during juglone stress. Exposure to juglone triggered changes in the transcript levels for several genes related to cell rescue and defense, with the majority of these genes potentially associated with chemical detoxification pathways, abiotic stress response pathway, cell wall formation and epigenetic mechanism. Molecular mechanisms for the allelochemical,juglone, in rice roots
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Project description:In the current study, we characterized an miRNA, OsmiR397, which was found to be associated with increased grain size, more rice panicle branching and higher grain productivity. We also elucidated the molecular mechanisms by which OsmiR397 increased grain yield. This miRNA downregulated the expression of its target gene, OsLAC, which then affected the sensitivity of plants to brassinosteroids. These results should be useful for breeding high-yield crops through genetic engineering. We performed RNA-seq on the young panicles of the wild-type, OXmiR397b and OXLAC plants and found that lots of brassinosteroid-related genes were differentially expressed between the three samples
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