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Quantitative proteomics of cytosolic and membrane-associated fractions of hypocotyl in Arabidopsis treated by ethylene

ABSTRACT: We performed quantitative proteomics to identify proteins present in cytosolic and membrane-associated fractions of etiolated hypocotyl in Arabidopsis plants (Col-0 vs. ein2-5).

INSTRUMENT(S):

ORGANISM(S): Arabidopsis Thaliana (mouse-ear Cress)

TISSUE(S): Hypocotyl

SUBMITTER: Youngwoo Lee

LAB HEAD: Daniel Szymanski

PROVIDER: PXD061207 | Pride | 2026-01-14

REPOSITORIES: Pride

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			Action	DRS
	C1-P_1_A.raw	Raw
	C1-S_1_A.raw	Raw
	C1-S_1_B.raw	Raw
	C2-P_1_A.raw	Raw
	C2-S_1_A.raw	Raw

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Publications

Rapid ethylene-triggered protein complex remodeling in dark-grown Arabidopsis hypocotyls.

Lee Youngwoo Y Park Hye Lin HL Yoon Gyeong Mee GM Szymanski Daniel B DB

Plant physiology 20251101 4

Protein-level cellular dynamics, including multimerization, play a crucial role in the rapid adaptation of plants during developmental transitions and environmental stresses. The gaseous phytohormone ethylene is a key regulator of rapid cellular growth. During soil emergence, etiolated seedlings undergo crucial morphological changes to their apical hooks and hypocotyls, with ethylene inhibiting hypocotyl axial elongation while promoting radial expansion. Ethylene triggers these growth responses ...[more]

PMID: 41396865

Similar Datasets

CFMS analysis of protein complex dynamics responding to ethylene treatment in etiolated Arabidopsis hypocotyl

Project description:Changes in protein multimerization stages as a response to ethylene treatment were investigated in etiolated Arabidopsis hypocotyl using Co-fractionation Mass spectrometry.

2026-01-14 | PXD061200 | Pride

Identification of molecular factors explaining decreased hypocotyl growth at low temperature

Project description:affy_hypoctemp_medicago - The characterization of several genotypes of the model Legume Medicago truncatula showed a genetic variability for germination and hypocotyl heterotrophic growth at low temperature and optimal temperature. The most important contrast was between the accessions Jemalong A17 and F83005.5. In order to find genes differently expressed between temperatures and genotypes, the present work focuses on transcriptome profiling during hypocotyl heterotrophic growth under low (10°C) and optimal (20°C) temperature conditions for both genotypes. We used Jemalong A17 and F83005.5 seeds coming from the Medicago truncatula Biological Resource Center in Montpellier, produced in 2006. Experiments were performed in the dark to mimic pre-emergence growth. Pots (6.5 cm diameter, 10 cm high) were incubated in growth chambers either at 10°C or 20°C. They were filled with 500g sand and 100ml of a nutrient solution for young seedlings growth (Saglio and Pradet, 1980). Per pot, five scarified seeds were sown at 1.5 cm depth. Seedlings were harvested at three times: 35°Cd (degree day), 50°Cd and 100°Cd. At each timepoint, about 50 seedlings were harvested and hypocotyl lengths was measured. Hypocotyl were cut and immediately frozen in liquid nitrogen for RNA extractions. Time course of 24 arrays - Medicago

2010-09-10 | E-GEOD-18449 | biostudies-arrayexpress

Effect of hit compounds on ethylene mutant eto1-4

Project description:Analysis of ethylene mutant (eto1-4) genome expression profile altered by ethylene antagonists. Results uncovered a significant number of genes that were co-regulated by the ethylene antagonists which may contribution on phenotype difference between WT and eto1-4. WT (Col-0) or ethylene mutant (eto1-4) were etiolated growth 3-day on 0.5x MS medium as control. Ethylene mutant (eto1-4) etiolated growth 3-day on 0.5x MS medium containing 10 Î¼M different ethylene antagoinsts were used as experimental set. Whole seedling was used for total RNA extraction and cDNA synthesis. cDNA labeling, array hybridization, and scanning followed by standard Affymetrix expression array protocol. Two independent sets of microarray analyses were performed in this assay.

2010-10-18 | E-GEOD-20897 | biostudies-arrayexpress

Proteomic analysis of soybean root including hypocotyl during recovery after drought stress

Project description:Soybean is a nutritionally important crop that exhibits reductions in growth and yields under drought stress. To investigate soybean responses during post-drought recovery, a gel-free proteomic technique was used to examine the protein profile. Two-day-old soybeans were stressed with drought for 4 days, recovered for 4 days, and root including hypocotyl was collected under drought and during the recovery stage. Morphological analysis revealed that growth was suppressed under drought stress that recovered following stress removal. Malondialdehyde content was increased under drought stress but returned to normal during the recovery stage. A total of 792 and 888 proteins were identified in control and drought-stressed root including hypocotyl during recovery stage, respectively. Based on the proteomic and cluster analyses, peroxidase and aldehyde dehydrogenase were significantly changed at analyzed time points under drought stress and during recovery. The activity of peroxidase was decreased under drought stress but increased during recovery. The activity of aldehyde dehydrogenase was increased under drought stress but returned to normal during the recovery stage. These results suggest that peroxidase and aldehyde dehydrogenase play key role in post-drought recovery in soybean by scavenging toxic reactive oxygen species and reducing harmful aldehydes load.

2016-06-16 | PXD003650 | Pride

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

A PIF-SAUR module safeguards hypocotyl elongation from ABA inhibition in the dark

Project description:Driven by cell elongation, hypocotyl growth is tightly controlled by light and responds to both external stimuli and endogenous hormonal pathways. Hypocotyls are responsive to the stress signalling hormone abscisic acid (ABA), which effectively inhibits cell elongation. However, how this regulation is connected to light signalling has been a subject of limited studies. Here, we show that, contrary to light-grown seedlings, hypocotyl elongation of dark-grown seedlings is ABA-insensitive. In the dark, hypocotyl sensitivity to ABA is restored in the constitutive photomorphogenic pifq and cop1-4 mutants, suggesting that an active light signalling pathway is necessary for hypocotyl responsiveness to ABA. Surprisingly, etiolated hypocotyls retain an intact ABA signalling pathway, as could be detected by the induction of ABI1 and RD29B transcripts in response to exogenous ABA, suggesting that inhibition of hypocotyl elongation occurs through a divergent path that can be inhibited by PIFs. Here, using RNA-seq analysis we identified a number of ABA differentially expressed genes (DEGs) that correlate with ABA inhibition of hypocotyl elongation. Among these DEGs a number of SMALL AUXIN-UP RNA (SAUR) genes that are known to directly repress D-CLADE TYPE 2C PROTEIN PHOSPHATASES (PP2C.D) were found. The abrogation of PP2CD.D2-SAUR interaction in the pp2c.d2/PP2C.D2M331K -GFP line, restored ABA sensitivity in the dark, suggesting that SAUR proteins, upregulated by PIFs, are sufficient to render hypocotyls insensitive to ABA. This hypocotyl-specific mechanism enables to promote growth towards the light at all costs, overriding ABA inhibition of cell elongation, to ensure subsequent seedling establishment and survival.

2025-05-22 | GSE283262 | GEO

Long Hypocotyl 1 mediates light regulation of adventitious root development in Arabidopsis

Project description:Adventitious root (AR) formation is controlled by both endogenous and environmental cues. Light is an important environmental factor that has been reported to promote plant root development. However, knowledge about the mechanisms controlling light-mediated AR formation in etiolated hypocotyl cuttings is not fully understood. In this study, we report that a light-induced photomorphogenic gene Long Hypocotyl 1 (HY1), regulates AR formation in Arabidopsis and rice. In Arabidopsis, plastid-localized AtHY1 in pericycle cells was capable of activating AR formation. Transcriptome profiling and genetic evidence revealed that Phytochrome B (AtPHYB) and Long Hypocotyl 5 (AtHY5) act downstream of HY1 to regulate AR formation, through the stimulation of auxin signaling and transport. However, in rice, AR emergence at stem node is inhibited by light upon submergence, opposite to its effects in Arabidopsis. We further showed that defective mutants of OsHY1, OsPHYB and OsHY5 showed enhanced AR emergence by upregulating the expression of OsGH3s and OsPIN1 genes. These findings uncover a opposite role of HY1 on AR development in responses to light between Arabidopsis and rice.

2025-10-20 | GSE280648 | GEO

Transcription profiling of Arabidopsis stem, leaf and hypocotyl tissue undergoing varying amounts of secondary cell wall synthesis

Project description:The aim of this experiment was to understand secondary cell wall formation as it is a major constituent of wood and plant fibres. To identify potential novel genes involved in this process, data has been generated from Arabidopsis stem, leaf and hypocotyl tissue undergoing varying amounts of secondary cell wall synthesis.

2006-01-01 | E-MEXP-265 | biostudies-arrayexpress

Ethylene-independent Promotion of Photomorphogenesis by Cytokinin Requires a Functional Cytokinin and Light Signaling Pathway.

Project description:The transition of skotomorphogenesis to photomorphogenesis is induced by the perception of light and is characterized by the inhibition of hypocotyl elongation and opening of cotyledons. Although it is known that the plant hormone cytokinin, when applied in high concentrations, inhibits hypocotyl elongation in the dark-grown Arabidopsis plants, it is unclear to what extent this response is the result of cytokinin alone or cytokinin-induced ethylene production. We show that treatment of etiolated seedlings in presence of ethylene inhibitors (eg. AgNO3) or treatment of the ethylene-resistant mutant ein2, resulted in a significant inhibition of hypocotyl elongation. This indicates that cytokinin induced de-etiolation is largely independent of ethylene and suggests a close connection between the cytokinin two component system and the light singalling networks. We show that this cytokinin signal is mainly mediated through the cytokinin receptor ARIBIDOPSIS HISTIDIN KINASE 3 (AHK3) and the ARABIDOPSIS RESPONSE REGULATORS 1 (ARR1) in combination with ARR12. Interestingly, mutation of COP1, DET1 and CIN4/COP10 renders plants insensitive to cytokinin and these factors are indispensable for the transcriptional response during cytokinin induced de-etiolation which indicates that a functional light signaling pathway is essential for this cytokinin response. In addition, the cytokinin effect on hypocotyl elongation is highly dependent on the ambient light conditions where higher light intensities causes a switch in the response to CK from an inhibitor to a promoter of hypocotyl elongation.

2018-10-01 | GSE108912 | GEO

Proteomic and morphological analyses of post-flooding recovery in soybean root exposed to aluminum oxide nanoparticles

Project description:To elucidate Al2O3 NPs role in recovery of soybean under flooding stress, gel-free proteomic technique was used. The proteomic analysis of root including hypocotyl at 2, and 4 days of flooding with 50 ppm Al2O3 NPs leading to subsequent removal as compared to flooding was performed.

2016-04-19 | PXD003372 | Pride

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