Metabolomics,Unknown,Transcriptomics,Genomics,Proteomics

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Changes in the transcriptome of smoke and butenolide treated germinating maize kernels

ABSTRACT: Smoke released from burning vegetation functions as an important environmental signal promoting the germination of many plant species following a fire . It not only promotes the germination of species from fire-prone habitats, but several species from non-fire-prone areas also respond, including some crops. Bioactivity-guided fractionation of smoke-water led to the identification of a highly active butenolide compound, 3-methyl-2H-furo[2,3-c]pyran-2-one. Several hypotheses have arisen regarding the molecular background of smoke and butenolide action. Contrary to the efforts to unravel the mode of action of smoke, the mechanism is still largely unknown. In this paper we demonstrate that although smoke-water and butenolide treatment of maize kernels results in a similar physiological response, the gene and protein expression patterns are quite different. Treatment with smoke-water enhanced the ubiquitination of proteins and activated protein-degradation-related genes. This effect was completely absent from butenolide-treated kernels, in which a specific aquaporin gene was distinctly upregulated. These findings indicate that other bioactive compounds present in smoke-water may act together, leading to accelerated protein turnover. The results highlight the importance of protein degradation and aquaporins in the seed germination process. Besides their obvious use in the sustainable agricultural practice, smoke and butenolide can be used in studies to gain further insight into the transcriptional changes during germination. 15 individual kernels from each of six biological replicates were chosen and equal amount of the aaRNA samples were pooled. Three technical replicates were applied at each time point for the microarray analysis. For the control versus butenolide experiment the samples were collected at 1.5, 3, 6, 9, 12 and 24 hours after treatment. For the control versus smoke experiment the samples were collected at 1.5, 3, 6, 9, 12, 24 and 27 hours after treatment. For the delayed experiment samples were collected after 3 or 6 hours after treatment.

ORGANISM(S): Zea mays

SUBMITTER: Endre SebestyÃ©n

PROVIDER: E-GEOD-17484 | biostudies-arrayexpress |

REPOSITORIES: biostudies-arrayexpress

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Project description:Sensing environmental cues is essential for plants in order to respond properly to, adapt to and survive changes in the environment and disturbances. Smoke-derived germination active compounds are important cues which provide a strong chemical signal to seeds in the soil seed bank about the available germination niche created by the passage of fire. The germination stimulatory activity can largely be attributed to the presence of the butenolide, 3-methyl-2H-furo[2,3-c]pyran-2-one (karrikinolide; KAR1). More recently, a related fire-borne butenolide, 3,4,5-trimethylfuran-2(5H)-one (inhibenolide A; InhA), was shown to have an inhibitory effect on germination. The aim of this study was to extensively characterize the interaction of these potent smoke-derived compounds in the highly KAR1-sensitive Lactuca sativa cv. M-bM-^@M-^XGrand RapidsM-bM-^@M-^Y achenes. A time course microarray analysis of KAR1- and InhA-treated achenes was performed using custom-made Agilent microarrays. Early time points for sampling the transcriptome were chosen by taking into account the fact that treatment with KAR1 is irreversible (by leaching with water) after 2 h, and that the KAR1-treated achenes enter an InhA-insensitive stage after 9 h. Therefore, samples were harvested after 2 and 10 h of initial exposure to 0.1 M-BM-5M KAR1 or 10 M-BM-5M InhA, and after 24 h, when germinated and non-germinating achenes could be distinguished visually. To assess the divergence between the expression patterns induced by the two compounds, a sample of achenes treated with 0.1 M-BM-5M KAR1 and 10 M-BM-5M InhA simultaneously, was harvested after 2 h. At 24 h, samples were collected from germinating and non-germinating achenes separately, and equal amounts of mRNA were pooled. Although this design implies that there is a small chance of losing data, our primary aim at 24 h was to screen for differences between the KAR1- and InhA-induced transcriptome. Achenes germinated in distilled water served as controls and were compared to the experimental samples treated as described above.

Project description:Aspergillus flavus is one of the major fungal molds that colonize peanut in the field and during storage. The impact to human and animal health and to economy in agriculture and commerce are significant since this mold produces the most potent natural toxins, aflatoxins, which are carcinogenic, mutagenic, immunosuppressive, and teratogenic. A strain of marine Bacillus megaterium isolated from the Yellow Sea of East China was evaluated for its effect to inhibit aflatoxin formation through down-regulating aflatoxin pathway gene expression in A. flavus as demonstrated by genechip analysis in liquid medium and peanuts. The results showed that aflatoxin accumulation in potato dextrose broth liquid medium and liquid minimal medium was almost totally (more than 98%) inhibited by B. megaterium. The expression of many of the aflatoxin biosynthetic genes in the fungus was confirmed to be turned down. Some of the target genes down-regulated by B. megaterium within the whole genome and within the aflatoxin pathway gene cluster (aflF, aflT, aflS, aflJ, aflL, aflX) were identified. These target genes could be used for controlling aflatoxin contamination in crops such as corn, cotton, and peanut. Importantly, the expression of the regulatory gene aflS was found to be significantly down-regulated. The effect of B. megaterium on aflatoxin biosynthesis and genes expression of pathogen was firstly tested in potato dextrose broth (PDB) and glucose minimal salts medium (MM). The cell suspension of B. megaterium (concentration in PDB and MM was finally adjusted to 108 CFU/ml) or sterile distilled water as a control was added into the 100 ml beaker flask containing 15 ml PDB or MM, respectively. Then 100 M-NM-<l of spore suspension (5 M-CM-^W 106 spores/ml) of A. flavus were added into each beaker flask. After 48 h of incubation at 28M-BM-0C at 200 rpm, mycelia were collected, fresh frozen with liquid nitrogen, ground to a fine powder in liquid nitrogen, and stored at -80M-BM-0C for further analysis. The effect of B. megaterium on aflatoxin biosynthesis and genes expression in the A. flavus fungal pathogen was also tested in two types of peanut kernels, UF 715133-1 and Jinhua 1012, respectively. Peanut kernels were wounded (6 mm diameter and approximately 3 mm deep) using a sterile borer and then 20 M-NM-<l of 1 M-CM-^W 108 CFU/ml cell suspension of B. megaterium was inoculated on wounded peanut kernels respectively. Sterile distilled water was also used for inoculation as control. Two hours after bacterial inoculation, 10 M-NM-<l A. flavus spore suspension was inoculated into each wound at a concentration of 106 spores/ml. The kernels were placed in artificial weather chamber to maintain high humidity (85%) and incubated at 28M-BM-0C for 7 days. Each treatment was replicated three times with 20 peanut kernels in each test. The mycelia on kernels were harvested at day 7 and fresh frozen immediately in liquid nitrogen, ground into powder, and stored at -80M-BM-0C for further analysis.

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Changes in the transcriptome of smoke and butenolide treated germinating maize kernels

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