Metabolomics,Unknown,Transcriptomics,Genomics,Proteomics

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Transcription profiling of barley exposed to low temperature stress

ABSTRACT: In this study we used the Affymetrix Barley 1 GeneChip to investigate transcriptome responses of barley cv. Morex to low temperature, including triplicated measurements of cold, freeze/thaw cycles and de-acclimation over 33 days. Experiment Overall Design: Plants were grown at 20ÂºC for seven days and subject to a symmetrical cycle of acclimation, cold, freeze-thaw, and deacclimation. Chilling began by decreasing the temperature overnight from 20ÂºC to 4ÂºC at a rate of 1.3ÂºCâ¢h-1 and maintaining temperatures of 4 ÂºC in the day and 2ÂºC at night for 5 days. Freeze-thaw cycling lasted 12 days with day temperatures of 4ÂºC and night temperatures gradually decreasing from -2ÂºC the first night to -4ÂºC for three nights and -10ÂºC for four nights, then recovering to -4ÂºC for three nights and -2ÂºC for one night. This treatment was designed to allow daily freeze-thaw cycling and protein synthesis. Chilling conditions (4ÂºC day, 2ÂºC night) were resumed for five days, followed by deacclimation with increasing temperature to 20ÂºC overnight and maintaining for three days. Sampling was done at four different times, each at the 11th hour of light to avoid circadian effects: 1) before chilling treatment, 2) five days after initiation of chilling treatment, 3) eight days into freeze-thaw treatment and 4) three days into de-acclimation.

ORGANISM(S): Hordeum vulgare

SUBMITTER: Livia Tommasini

PROVIDER: E-GEOD-6993 | biostudies-arrayexpress |

REPOSITORIES: biostudies-arrayexpress

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Project description:Saccharomyces cerevisiae is exposed to freeze-thaw stress in commercial processes including frozen dough baking. The cell viability and fermentation activity after freeze-thaw were dramatically decreased due to freeze-thaw injury. Because freeze-thaw injury involves complex phenomena, the mechanisms of it are not fully understood. We attempted to analyze the mechanisms of freeze-thaw injury by indirect gene expression analysis during post-thaw incubation after freeze-thaw treatment using DNA microarray profiling. The results showed that a high frequency of the genes involved in the homeostasis of metal ions were up-regulated depending on the freezing period. The phenotype of the deletion mutants of the up-regulated genes extracted by indirect gene expression analysis was assessed. The deletion strains of the MAC1 and CTR1 genes involved in copper ion homeostasis exhibited freeze-thaw sensitivity, suggesting that copper ion homeostasis is required for freeze-thaw tolerance. Supplementation with copper ions during post-thaw incubation increased intracellular superoxide dismutase activity. Inverse correlated with intracellular superoxide dismutase activity, intracellular levels of reactive oxygen species were decreased. Moreover, cell viability increased by supplementation with copper ions under specific assessment conditions. This study suggested that insufficiency of copper ion homeostasis may be one of the causes of freeze-thaw injury. Total RNA was extracted from the stress-treated yeast cells by using a hot phenol method. Poly(A)+ RNA was enriched from total RNA by using an Oligotex dT30 (Super) mRNA purification kit (Takara Bio, Ohtsu, Japan). cDNA synthesis, cRNA synthesis, and labeling were performed according to the Affymetrix user’s manual (Affymetrix, Santa Clara, USA). Biotinyated cRNA was fragmented and then used as a probe.Affimetrix Yeast Genome 2.0 arrays (Affymetrix) were used as DNA microarrays. All experiments were done in triplicate independently.

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Transcription profiling of barley exposed to low temperature stress

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