Metabolomics,Unknown,Transcriptomics,Genomics,Proteomics

Dataset Information

Autotoxicity mechanism of Oryza Sativa: Microarray analysis of rice plants in response to allelochemical ferulic acid

ABSTRACT: 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).

ORGANISM(S): Oryza sativa

SUBMITTER: Wen-Chang Chi

PROVIDER: E-GEOD-34899 | biostudies-arrayexpress |

REPOSITORIES: biostudies-arrayexpress

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Publications

Autotoxicity mechanism of Oryza sativa: transcriptome response in rice roots exposed to ferulic acid.

Chi Wen-Chang WC Chen Yun-An YA Hsiung Yu-Chywan YC Fu Shih-Feng SF Chou Chang-Hung CH Trinh Ngoc Nam NN Chen Ying-Chih YC Huang Hao-Jen HJ

BMC genomics 20130525

<h4>Background</h4>Autotoxicity plays an important role in regulating crop yield and quality. To help characterize the autotoxicity mechanism of rice, we performed a large-scale, transcriptomic analysis of the rice root response to ferulic acid, an autotoxin from rice straw.<h4>Results</h4>Root growth rate was decreased and reactive oxygen species, calcium content and lipoxygenase activity were increased with increasing ferulic acid concentration in roots. Transcriptome analysis revealed more tr ...[more]

PMID: 23705659

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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. Biofuel toxicity must also be overcome to allow for efficient production of next generation biofuels such as butanol, isopropanol, and others for widespread usage. Currently, these inhibitory compounds must be removed through additional downstream processing or sufficiently diluted to create environments suitable for most industrially important microbial strains. This study explores the high ferulic acid and n-butanol 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 and butanol 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 contrast to the ferulic acid stress response, butanol addition to growing cultures uniquely induced the entire fatty acid synthesis pathway in the midst of a generalized stress response. Overexpression of the rate-limiting acetyl-CoA carboxylase subunits (AccABCD) in E. coli to increase lipid synthesis had no effect on butanol tolerance, suggesting that additional engineering is necessary to produce sufficient levels of appropriate fatty acids to confer butanol tolerance. Several promising routes for understanding both phenolic acid and butanol tolerance have been identified based upon these findings. These insights may be used to guide further engineering of model industrial organisms to better tolerate both classes of inhibitors in processed biomass used for biofuel production. Cultures were grown to OD ~ 0.2 in MRS media (baffled flasks), T = 30 C, 100 rpm. Butanol was then added to the cultures. Samples were harvested 15, 75, and 135 min after butanol addition. Each time point has 3 biological replicates, and dye swaps were incorporated into the microarray experiments.

Dataset Information

Autotoxicity mechanism of Oryza Sativa: Microarray analysis of rice plants in response to allelochemical ferulic acid

Publications

Autotoxicity mechanism of Oryza sativa: transcriptome response in rice roots exposed to ferulic acid.

Similar Datasets

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