Project description:Phytochromes are red/far-red light photoreceptors. We sought to test at the transcriptomic level if Arabidopsis mutants lacking all phytochromes (from phyA to phyE), or just retaining trace levels of phyC, had transcriptional response to red light exposure.
Project description:Phytochromes are red/far-red light photoreceptors. We sought to test at the transcriptomic level if Arabidopsis mutants lacking all phytochromes (from phyA to phyE), or just retaining trace levels of phyC, had transcriptional response to red light exposure. phyABCDE and phyABDE mutants were grown for 4 days in darkness (D), or under continuous red light at 50 µmol m-2 s-1 (R50), or in darkness followed by 2 hr of red light exposure on day 4 (DR2h). Differentially expressed genes of the mutants in response to red light were compared to those of wild type obtained previously {Hu et al. (2009) Molecular Plant, 2: 166-182}. Three biological replicates were employed for dark and Rc-grown samples, and 2 biological replicates for DR2h samples, thus 8 samples were used for each mutant genotype. It needs to be pointed out that 5 of the 6 WT samples (from WT-D-2 to WT-R50-2) had previously been deposited with GEO accessions GSM226267, GSM226268, GSM226269, GSM226278 and GSM226279. Their cRNA samples were synthesized and labeled with the Affymetrix GeneChip® Expression Analysis kits (One-cycle target labeling and control reagents). They are included in this series of study for convenient comparison, with newly assigned accessions from GSM784837 to GSM784841. The more recent GeneChip 3' IVT Express Kit (Affymetrix) was used to synthesize and label aRNA for one new WT sample (WT-D-1)(GSM784836) and all mutant samples.
Project description:Environmental stimuli-triggered stomatal movement is a key physiological process that regulates CO<sub>2</sub> uptake and water loss in plants. Stomata are defined by pairs of guard cells that perceive and transduce external signals, leading to cellular volume changes and consequent stomatal aperture change. Within the visible light spectrum, red light induces stomatal opening in intact leaves. However, there has been debate regarding the extent to which red-light-induced stomatal opening arises from direct guard cell sensing of red light versus indirect responses as a result of red light influences on mesophyll photosynthesis. Here we identify conditions that result in red-light-stimulated stomatal opening in isolated epidermal peels and enlargement of protoplasts, firmly establishing a direct guard cell response to red light. We then employ metabolomics workflows utilizing gas chromatography mass spectrometry and liquid chromatography mass spectrometry for metabolite profiling and identification of Arabidopsis guard cell metabolic signatures in response to red light in the absence of the mesophyll. We quantified 223 metabolites in Arabidopsis guard cells, with 104 found to be red light responsive. These red-light-modulated metabolites participate in the tricarboxylic acid cycle, carbon balance, phytohormone biosynthesis and redox homeostasis. We next analyzed selected Arabidopsis mutants, and discovered that stomatal opening response to red light is correlated with a decrease in guard cell abscisic acid content and an increase in jasmonic acid content. The red-light-modulated guard cell metabolome reported here provides fundamental information concerning autonomous red light signaling pathways in guard cells.
Project description:RNAseq profiling of eight transcription factor mutants during germination in Arabidopsis, at 24 h in the light (after 48h of stratification).
Project description:We report the transcriptomic response of Arabidopsis thaliana seedlings grown in continuous white light, darkness or darkness and 1 hour of red light
Project description:Transcriptional profiling of Arabidopsis far-red light pulse treated seeds comparing luh mutant with wild type (Col-0). Seeds were imbibed within 1 hr under white light and treated far-red light pulse for 5 min followed by 12 hr dark incubation. Goal was to determine the effects of LUH as transcriptional co-regulator during seed germination process.
Project description:This experiment was a time course performed over 24 hours to look at the effects on gene expression of exposure to low red:far-red ratio light in Arabidopsis thaliana plants. In this way genes involved in the shade avoidance response might be identified. This experiment was designed for gene identification only and containes no replicates,genes identified were verified by quantitative PCR for publication.
Project description:Transcriptional profiling of Arabidopsis thaliana Ler wildtype and eid3 (empfindlicher im dunkelroten Licht 3) mutant seedlings in darkness and 45 min after a red-light pulse.
Project description:Exploring miRNA-related antisense transcription in Arabidopsis through RNA transcript profiling of smRNA pathway-defective mutants on a custom high-resolution oligonucleotide array.
Project description:The cold acclimation process is regulated by many factors like ambient temperature, day length, light intensity, or hormonal status. Experiments with plants grown under different light-quality conditions indicate that the plant response to cold is also a light-quality-dependent process. Here, the role of light quality in the cold response was studied in one-month-old Arabidopsis thaliana (Col‐0) plants exposed for one week to 4 °C at short‐day conditions under white (100 and 20 μmol m‐2s‐1), blue or red (20 μmol m‐2s‐1) light conditions. An upregulated expression of CBF1, an inhibition of photosynthesis, and an increase in membrane damage showed that blue light enhanced the effect of low temperature. Interestingly, cold-treated plants under blue and red light showed only limited freezing tolerance compared to white light cold-treated plants. Next, the specificity of the light quality signal in cold response was evaluated in Arabidopsis accessions originating from different and contrasting latitudes. In all but one Arabidopsis accessions, blue light increased the effect of cold on photosynthetic parameters and electrolyte leakage. This effect was not found for Ws-0, which lacks functional CRY2 protein, indicating its role in the cold response. Proteomics data confirmed significant differences between red and blue light treated plants at low temperature and showed that the cold response is highly accession specific. In general, blue light increased mainly the cold-stress related proteins and red light induced higher expression of chloroplast-related proteins, which correlated with higher photosynthetic parameters in red light cold-treated plants. Altogether, our data suggest that light modulates two distinct mechanisms during the cold treatment - red light driven cell function maintaining program and blue light activated specific cold response. The importance of mutual complementarity of these mechanisms was demonstrated by significantly higher freezing tolerance of cold-treated plants under white light.