Phytochrome A-mediated shade avoidance responses
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ABSTRACT:
ORGANISM(S): Arabidopsis thaliana
PROVIDER: GSE55899 | GEO | 2019/12/21
REPOSITORIES: GEO
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Project description:Low reduced red:far-red ratio [R:FR] signaling through phytochromes induces shade avoidance responses, including petiole elongation. Jasmonic acid-mediated defense against herbivores and pathogens is inhibited under these conditions. Using microarrays we studied the crosstalk between low R:FR and JA at the global gene expression level in Arabidopsis thaliana.
2012-05-01 | GSE35700 | GEO
Project description:Plants grown at high densities perceive a decrease in the red to far-red (R:FR) ratio of incoming light, resulting from absorption of red light by canopy leaves and reflection of far-red light from neighboring plants. These changes in light quality trigger a series of responses known collectively as the shade avoidance syndrome. During shade avoidance, stems elongate at the expense of leaf and storage organ expansion, there is reduced branching, and flowering is accelerated. We identified several loci in Arabidopsis, mutations in which lead to plants defective in multiple shade avoidance outputs. Here we describe SAV3, an aminotransferase, and show that SAV3 catalyzes the formation of indole-3-pyruvic acid (IPA) from L-tryptophan (L-Trp), the first step in a previously proposed, but uncharacterized, auxin biosynthetic pathway. This pathway can be rapidly deployed to biosynthesize auxin at the high levels required to initiate the multiple changes in body plan associated with shade avoidance. Experiment Overall Design: Wild type Col-0, sav3-2 and sav1-1 seedlings were used here. They were treated with or without 1hr of low R:FR light (R:FR ratio=0.7). Three independent biological replicates were used.
2008-06-16 | E-GEOD-9816 | biostudies-arrayexpress
Project description:Plants grown at high densities perceive a decrease in the red to far-red (R:FR) ratio of incoming light, resulting from absorption of red light by canopy leaves and reflection of far-red light from neighboring plants. These changes in light quality trigger a series of responses known collectively as the shade avoidance syndrome. During shade avoidance, stems elongate at the expense of leaf and storage organ expansion, there is reduced branching, and flowering is accelerated. We identified several loci in Arabidopsis, mutations in which lead to plants defective in multiple shade avoidance outputs. Here we describe SAV3, an aminotransferase, and show that SAV3 catalyzes the formation of indole-3-pyruvic acid (IPA) from L-tryptophan (L-Trp), the first step in a previously proposed, but uncharacterized, auxin biosynthetic pathway. This pathway can be rapidly deployed to biosynthesize auxin at the high levels required to initiate the multiple changes in body plan associated with shade avoidance. Keywords: shade avoidance auxin brassinosteroid
2008-04-01 | GSE9816 | GEO
Project description:Low reduced red:far-red ratio [R:FR] signaling through phytochromes induces shade avoidance responses, including petiole elongation. Jasmonic acid-mediated defense against herbivores and pathogens is inhibited under these conditions. Using microarrays we studied the crosstalk between low R:FR and JA at the global gene expression level in Arabidopsis thaliana. Plants were exposed for 2 h. to the following treatments: high R/FR with mock spray, low R/FR with mock spray, high R/FR with JA spray, low R/FR with JA spray. Gene expression was determined in petioles.
2012-04-30 | E-GEOD-35700 | biostudies-arrayexpress
Project description:Plants respond to changes in the red:far red ratio (R:FR) of incident light. A reduction in this ratio (increase in FR) results in the Shade Avoidance Response (SAR) with associated changes in gene expression. The Phyotchrome-Interacting Factors (PIFs) are bHLH transcription factors known to be involved in the SAR. An analysis of changes in gene expression in WT and quadruple pif1pif3pif4pif5 (pifq; Leivar et al., 2008 (PMID 19920208)) mutant seedlings in response to an increase in FR should identify primary targets of PIF signaling.
2012-08-02 | GSE28297 | GEO
Project description:To study the transcriptomic profile of wt and brc1 mutant axillary buds during the shade avoidance response, we simulated a canopy shade with a low R/FR light ratio. We treated plants with white light supplemented with far-red light (Red light = 29 μeinstein · m-2 seg-1, Far-Red light= 146 μeinstein · m-2 seg-1) for 8 hours. Control plants were left for 8 hours in white light (Red light = 29 μeinstein · m-2 seg-1, Far-Red light= 2.2 μeinstein · m-2 seg-1) .
2013-02-28 | GSE27273 | GEO
Project description:To study the transcriptomic profile of wt and brc1 mutant axillary buds during the shade avoidance response, we simulated a canopy shade with a low R/FR light ratio. We treated plants with white light supplemented with far-red light (Red light = 29 μeinstein · m-2 seg-1, Far-Red light= 146 μeinstein · m-2 seg-1) for 8 hours. Control plants were left for 8 hours in white light (Red light = 29 μeinstein · m-2 seg-1, Far-Red light= 2.2 μeinstein · m-2 seg-1) . Six biological replicates of 7-8 plants were collected for each genotype and condition (wt WL, wt FR, brc1 WL, brc1 FR). Samples were compared wt WL vs wt FR and brc1 WL vs brc1 FR.
2013-02-28 | E-GEOD-27273 | biostudies-arrayexpress
Project description:The goal of this work was to investigate oxidative stress responses of Arabidopsis to low red to far-red ratios of light as a signal of competition using a biological weedy and an artificial source of far-red light. More specifically, elucidation of the signaling role of singlet oxygen in Arabidopsis under low red-to far-red light environments was the major objective of this work. Oxidative stress responses of Arabidopsis to low red (R) to far-red (FR) signals (R:FR ≈ 0.3), generated by a biological weedy and an artificial source of FR light, were compared with a weed-free control (R:FR ≈1.4). In the low R:FR treatments, induction of the shade avoidance responses coincided with increased singlet oxygen (1O2) production and decreased level of superoxide and superoxide dismutase activity. Although the increase of 1O2 was not due to protochlorophyllide accumulation and did not result in cell death, treatments with the 1O2 generator 5-aminolevulinic acid increased sensitivity to cell death. Transcriptome responses minimally resembled those reported in four Arabidopsis 1O2 generating systems such that only few genes (6 out of 1931) were consistently up-regulated supporting the specificity of 1O2 signaling. Moreover, suppressors of jasmonate accumulation, including the 1O2-responsive amidohydrolase ILL6, the sulfotransferase ST2a, which are involved in prioritization of elongation growth versus defense were consistently up-regulated. Our data support a model in which photoreceptors connect low R:FR light cues to the JA signaling pathway. Repression of bioactive JAs via the amidohydrolase ILL6, and sulfotransferase ST2a may promote the shade avoidance (versus defense) and 1O2 acclimation (versus cell death) responses to competition cues.
2022-09-14 | GSE213185 | GEO
Project description:Plants respond to changes in the red:far red ratio (R:FR) of incident light. A reduction in this ratio (increase in FR) results in the Shade Avoidance Response (SAR) with associated changes in gene expression. The Phyotchrome-Interacting Factors (PIFs) are bHLH transcription factors known to be involved in the SAR. An analysis of changes in gene expression in WT and quadruple pif1pif3pif4pif5 (pifq; Leivar et al., 2008 (PMID 19920208)) mutant seedlings in response to an increase in FR should identify primary targets of PIF signaling. We used microarrays to examine the SAR in WT (Columbia) and pifq mutant Arabidopsis seedlings. Arabidopsis WT and pifq mutant seeds were plated on GM medium without sucrose at room temperature. During this procedure, the seeds were routinely exposed to white light (WL) for a total of 1.5 hours after imbibition. Seeds were then stratified for 5 days at 4ºC in darkness, and then grown in WL (19 umol/m2/s, R/FR ratio of 6.48) for 2 days at 21°C (WL0 samples). Two-day-old WL-grown seedlings were then maintained in the same fluence rate of WL supplemented with far-red light (WL-FR, R/FR ratio of 0.006) for 1 (FR1), 3 (FR3) or 24 (FR24) hours before harvesting. Control seedlings were also maintained in parallel in the same fluence rate of WL for 24h (WL24) before harvesting. Three different biological replicates of each treatment were grown separately and extracted, processed, and analyzed independently.
2012-08-01 | E-GEOD-28297 | biostudies-arrayexpress
Project description:Aim of the experiment is the identification of genes differentially regulated in phyA seedlings relative to wild type after prolonged exposure to low R/FR. To this end, gene expression changes were analysed in Arabidopsis wild-type and phyA knock-out mutant seedlings exposed to low R/FR light. The experiment was designed to enable comparison between the different genotypes exposed or not exposed to low R/FR light.
2013-07-29 | E-MEXP-3267 | biostudies-arrayexpress