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Metabolomics,Unknown,Transcriptomics,Genomics,Proteomics

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The effect of sucrose and sulfamethoxazole on the Arabidopsis transcriptome

ABSTRACT: A chemical screen was performed in search of compounds that modify plant responses to sucrose. This screen uncovered that sulfamethoxazole (SMX), a folate biosynthesis inhibitor, acted synergistically with sucrose to inhibit hypocotyl elongation, suggesting interaction between these two pathways. Transcriptome analysis was performed to identify changes in transcript abundance that may underpin crosstalk between sucrose and SMX. Three-day-old dark-grown seedlings were treated to sucrose and SMX at concentrations that induced no change in hypocotyl elongation when administered independently, yet restricted elongation when both were present in the growth media (10mM and 0.2µM, respectively). This analysis uncovered multiple core auxin signalling components that exhibit altered transcript abundance in response to co-treatment with sucrose and SMX, suggesting that auxin signalling mediates crosstalk between these two pathways. This study highlights an input through which metabolic status can shape plant growth and development through hormone signalling. 12 arrays total. Three arrays as non-treated control, three arrays from seedlings raised in presence of 0.2µM SMX, three arrays from seedlings raised in presence of 10mM sucrose, and three arrays from seeldings raised in presence of both 10mM sucrose and 0.2µM SMX. Three biological replicates were produced for each growth treatment.

ORGANISM(S): Arabidopsis thaliana

SUBMITTER: Malcolm Campbell

PROVIDER: E-GEOD-37484 | biostudies-arrayexpress |

REPOSITORIES: biostudies-arrayexpress

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The effect of sucrose and sulfamethoxazole on the Arabidopsis transcriptome

Project description:A chemical screen was performed in search of compounds that modify plant responses to sucrose. This screen uncovered that sulfamethoxazole (SMX), a folate biosynthesis inhibitor, acted synergistically with sucrose to inhibit hypocotyl elongation, suggesting interaction between these two pathways. Transcriptome analysis was performed to identify changes in transcript abundance that may underpin crosstalk between sucrose and SMX. Three-day-old dark-grown seedlings were treated to sucrose and SMX at concentrations that induced no change in hypocotyl elongation when administered independently, yet restricted elongation when both were present in the growth media (10mM and 0.2µM, respectively). This analysis uncovered multiple core auxin signalling components that exhibit altered transcript abundance in response to co-treatment with sucrose and SMX, suggesting that auxin signalling mediates crosstalk between these two pathways. This study highlights an input through which metabolic status can shape plant growth and development through hormone signalling.

2013-06-30 | GSE37484 | GEO

Arabidopsis thaliana

Project description:Arabidopsis seedlings collected during hypocotyl elongation and hypocotyl stasis

| PRJNA125845 | ENA

Arabidopsis seedlings collected during hypocotyl elongation and hypocotyl stasis

Project description:The hypocotyl of Arabidopsis seedlings shows rhythmic periods of elongation. The patterns of elongation are controlled by a combination of internal factors, such as the circadian clock, and external factors such as light. In a previous study we had found that two transcription factors, PIF4 and PIF5 are important integrators of clock and light signals for the control of elongation. Here we use microarrays to find genes that are correlated with elongation and that are controlled by PIF4 and/or PIF5. Arabidopsis seedlings grown under short day conditions for three days were transferred to SD/3 conditions (160 min light: 320 min dark cycles) from the dawn of the fourth day. Seedlings were then collected during periods of hypocotyl elongation and stasis for three days. There are two types of replication: temporal and independent experiments. For temporal replication, samples collected at the same time of day on subsequent days were used as replicates. In addition, replicate samples were collected in two independent time courses for most time points. Col and CCA1OX samples from the first time course for time points 280, 1240, 1720, 2680, 3160, and 4120 were originally deposited under GEO Series GSE6906; they have been re-analyzed for this study. Each sample consists of multiple pooled seedlings.

2011-03-31 | E-GEOD-21684 | biostudies-arrayexpress

Analyses of genes regulated by the N-terminal photolyase homology region (CNT1/PHR) of CRY1 by RNA-seq

Project description:Total RNA was extracted from samples including 35S::CNT1-NLS-YFP;cry1 and 35S::CNT1-G283E-NLS-YFP;cry1 seedlings grown in continuous blue light and subjected to high throughput sequencing. Previous studies reported that the C-terminal domain of CRY1 regulates hypocotyl elongation and blue light-regulated genes. This study reveals that CNT1 overexpression also regulates blue light-regulated genes, supporting the role of CNT1 in hypocotyl elongation at transcriptomic level.

2016-07-25 | GSE59763 | GEO

Transcriptome analysis of calcium-regulated genes in relation to broccoli hypocotyl cell expansion

Project description:We report the application of RNA-seq to uncover the underlying mechanism of 10 mM calcium chloride spray on broccoli seedlings (Brassica oleracea var. italic) boosted the hypocotyl elongation and delayed the senescence.

2017-09-25 | GSE73455 | GEO

Hypocotyl and cotyledon transcriptome in Arabidopsis thaliana treated with 1 ppm ethylene and shade (low PAR, low blue and low R:FR)

Project description:Plants have evolved shoot elongation mechanisms to escape from diverse environmental stresses such as flooding and vegetative shade. The apparent similarity in growth responses suggests possible convergence of the signalling pathways. Shoot elongation is mediated by passive ethylene accumulating in flooded plant organs and by changes in light quality and quantity under vegetation shade. Here we study hypocotyl elongation as a proxy for shoot elongation and delineated Arabidopsis hypocotyl length kinetics in response to ethylene and shade. Based on these kinetics, we further investigated ethylene and shade-induced genome-wide gene expression changes in hypocotyls and cotyledons separately. Both treatments induced a more extensive transcriptome reconfiguration in the hypocotyls compared to the cotyledons. Bioinformatics analyses suggested contrasting regulation of growth promotion- and photosynthesis-related genes. These analyses also suggested an induction of auxin, brassinosteroid and gibberellin signatures and the involvement of several candidate regulators in the elongating hypocotyls. Pharmacological and mutant analyses confirmed the functional involvement of several of these candidate genes and physiological control points in regulating stress-escape responses to different environmental stimuli. We discuss how these signaling networks might be integrated and conclude that plants, when facing different stresses, utilise a conserved set of transcriptionally regulated genes to modulate and fine tune growth. 1 day old Arabidopsis seedlings were subjected to control, ethylene and shade conditions. Hypocotyl and cotyledon tissues were harvested at 1.5 h, 13.5 h and 25.5 h of treatment time respectively. Microarray hybridization was carried out with 3 biological replicates (collected over 3 independent experiments) of each sample using the Affymetrix Arabidopsis Gene 1.1 ST platform.

2016-06-10 | E-GEOD-83212 | biostudies-arrayexpress

Analyses of genes regulated by the N-terminal photolyase homology region (CNT1/PHR) of CRY1 by RNA-seq

2016-07-25 | E-GEOD-59763 | biostudies-arrayexpress

Transcription profiling of the1, prc1, prc1_the1 and prc1_the2 gene knockout Arabidopsis dark-grown hypocotyls to identify genes involved in cell wall integrity signalling

Project description:Inhibition of cellulose synthesis by chemical inhibitors or in a mutant background leads to rapid inhibition of cell elongation. This inhibition appears to be an active process, which involves feedback signalling from the cell wall. We have isolated two loci THE1 and THE2, which are identified by mutations that partially suppress the dark-grown hypocotyl phenotype in a mutant background for cellulose synthase catalytic subunit CESA6_PROCUSTE1. THE1 encodes a receptor kinase and may play a role in this feedback signalling process. To identify genes that are regulated by THE1 and THE2, we compared the transcript profiles of 5 day-old dark-grown seedlings of the1-1_prc1-1 with prc1-1 ; the1-3_prc1-8 with prc1-8 ; prc1-8 or the1-3 with WS and the2-1_prc1-1 with prc1-1.

2007-03-31 | E-MEXP-638 | biostudies-arrayexpress

Transcriptomics of the plant growth regulator Heatin

Project description:Temperature passively affects many biological processes. It is therefore challenging to study dedicated temperature signalling pathways orchestrating plant thermomorphogenesis; a suite of elongation growth-based adaptations that enhance leaf cooling capacity. Following a chemical genetics approach, we screened a chemical library for compounds that restored abolished hypocotyl elongation in the pif4-2 deficient mutant background in the model plant Arabidopsis thaliana. The small aromatic compound ‘Heatin' (N'-[(2-hydroxy-1-naphthyl)methylene]-2-(1-naphthylamino)propanohydrazide), with 1-aminomethyl-2-naphthol, as minimal active moiety, was isolated as potent enhancer of elongation growth. Here we assessed the transcriptomic changes induced by the compound, by supplementing the MS-agar growth medium with Heatin compared to DMSO solvent, in whole seedlings of the Col-0 wild type background in control (22oC) and high ambient temperature conditions (27oC).

2019-12-01 | GSE130964 | GEO

Arabidopsis seedlings collected during hypocotyl elongation and hypocotyl stasis

2011-03-31 | GSE21684 | GEO

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