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

ABSTRACT: 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.

ORGANISM(S): Arabidopsis thaliana

PROVIDER: GSE83212 | GEO | 2016/06/10

SECONDARY ACCESSION(S): PRJNA325269

REPOSITORIES: GEO

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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

Spatiotemporal analysis of shade-induced transcriptional reprogramming in Arabidopsis reveals patterns underlying organ-specific growth

Project description:In response to neighbor proximity plants increase growth of specific organs (e.g. hypocotyl) to enhance access to sunlight. Shade enhances the activity of Phytochrome Interacting Factors (PIFs) by releasing those bHLH transcription factors from phytochrome B-mediated inhibition. PIFs promote elongation by inducing auxin production in cotyledons. In order to elucidate spatiotemporal aspects of the neighbor proximity response, we analyzed changes in transcript abundance at different time points during a shade treatment in dissected cotyledons and hypocotyls. We concentrated our analysis on these two organs because the former is considered as the primary shade-sensing organ while elongation is rapidly triggered in the hypocotyl. We conclude that PIFs initiate transcriptional reprogramming in both organs within 15 minutes comprising regulated expression of several early auxin response genes. This suggests that hypocotyl growth is elicited by both local and distal auxin signals. With time the transcriptional response diverges increasingly between organs. We identify genes whose differential expression may underlie organ-specific elongation. Finally, we uncover a growth promotion gene expression signature shared between responses to different environments and organs.

2017-01-17 | GSE81202 | GEO

Arabidopsis SAURs Are Critical for Differential Light Regulation of the Development of Various Organs

Project description:During de-etiolation of Arabidopsis seedlings, light promotes the expansion of cotyledons but inhibits the elongation of hypocotyls. The mechanism of this differential regulation of cell enlargement is unclear. Our organ-specific transcriptomic analysis identified 32 Small Auxin Up RNA (SAUR) genes whose transcripts were light-induced in cotyledons and/or repressed in hypocotyls. We therefore named these SAURs as lirSAURs. Both overexpression and mutation analyses demonstrated that lirSAURs could promote cotyledon expansion and opening and enhance hypocotyl elongation, possibly by inhibiting phosphatase activity of PP2C-Ds. Light reduced auxin levels to down-regulate the expression of lirSAURs in hypocotyls. Further, phytochrome-interacting factors (PIFs) were shown

2016-05-03 | GSE79576 | GEO

phytochrome A-mediated shade avoidance responses

Project description:Arabidopsis is a shade avioding plant. Under simulated shade light with reduced red-to-far red (R:FR) ratio around 0.7, hypocotyls of Arabidopsis seedlings elongate, which is one of the typical shade avoidance responses.We discovered that when the R:FR ratio further decreases to around 0.1 (strong shade), the shade-induced elongation of hypocotyl is abolished and phytochrome A (phyA) mediates this response.In this study, we aim to examine the difference between shade and strong shade treatment and uncover the role of phyA in regulating the shade avoidance responses.

2019-12-21 | GSE55899 | GEO

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

A combination of plasma membrane sterol biosynthesis and autophagy is required for shade-induced hypocotyl elongation

Project description:We hypothesized a convergence of transcriptome profiles in hypocotyls of low blue light (LB) or low red/far red light (LRFR) treated seedlings as both conditions trigger hypocotyl cell elongation. To test this hypothesis, we did a transcriptome analysis in of 5d-old long-day (LD)-grown Col-0 (wild type, WT), pif457, and yuc2589 seedlings treated for 3 hours with LB, LRFR or remaining in the same light condition (WL). We used dissected cotyledons and hypocotyls to characterize the LB and LRFR response in both organs and determine their dependency on PIFs and YUC-mediated auxin biosynthesis.

2022-08-08 | GSE174655 | GEO

Auxin signaling in the epidermis regulates stem growth via interactions with the brassinosteroid pathway

Project description:Growth of a complex multicellular organism requires coordinated changes in diverse cell types. These cellular changes generate organs of the correct size, shape and functionality. During plant development, the growth hormone auxin induces stem elongation; however, which cell types of the stem perceive the auxin signal and contribute to organ growth is poorly understood. Here, we show that auxin signalling is required in many cell types for correct hypocotyl stem growth, with a key role for the epidermis. Combining genetic manipulations in Arabidopsis thaliana with transcriptional profiling of the hypocotyl epidermis from Brassica rapa, we show that auxin functions in the epidermis in part by inducing activity of the locally-acting, growth-promoting brassinosteroid pathway. Our findings clarify cell-specific auxin function in the hypocotyl, and highlight the complexity of cell-type interactions within a growing organ. We performed whole-genome transcriptome (mRNA-Seq) on 5 d-old W light-grown Arabidopsis thaliana plants (CER6pro>>axr3-1::mCit experimental plants and UAS::axr3-1::mCit hemizygous control plants; whole-seedling tissue) treated for 4 h W light or low R:FR shade. In addition, we performed mRNA-Seq on 4 d-old Brassica rapa plants (FPsc strain) treated for 9 h W light or shade. Brassica tissues collected were hypocotyl epidermal peels or whole hypocotyls.

2016-06-30 | E-GEOD-79881 | biostudies-arrayexpress

Temporal and spatial frameworks supporting plant responses to vegetation proximity

Project description:After perception of vegetation proximity by the phytochrome photoreceptors, shade-avoider plants initiate a set of responses known as the Shade Avoidance Syndrome (SAS). Shade perception by the phytochrome B (phyB) photoreceptor unleashes the PHYTOCHROME INTERACTING FACTORs (PIFs) and initiates SAS responses. In Arabidopsis thaliana seedlings, shade perception involves rapid and massive changes in gene expression, increases auxin production and promotes hypocotyl elongation. Other components, such as phyA and ELONGATED HYPOCOTYL 5 (HY5), also participate in the shade regulation of the hypocotyl elongation response by repressing it. However, it remains unclear why and how so many regulators with either positive or negative activities modulate the same response. Our physiological, genetic, cellular and transcriptomic analyses showed that (1) these components are organized in two main branches or modules (phyA/HY5 and PIFs/HFR1/SAV3) and (2) the connection between them is dynamic and changes with the time of shade exposure. We propose a model for the regulation of shade-induced hypocotyl elongation in which the temporal and spatial functional importance of the various SAS regulators analyzed in here helps to explain the co-existence of differentiated regulatory branches with overlapping activities. Despite the temporal differences observed between phyA, HY5 and PIFs/HFR1/SAV3, their activities overlap and eventually converge in controlling hypocotyl elongation. Hence, we aimed to further investigate possible convergence points between these two groups of regulators.To expand our understanding of the role and interaction of HY5 and PIF4, PIF5 and PIF7 (PIF457) activities, we carried out RNA sequencing (RNA-seq) of seedlings exposed to different times of shade exposure of four genotypes: wild-type (Col-0), the single mutant hy5, the triple pif457 and the quadruple hy5 pif457.

2024-08-26 | GSE268032 | GEO

Arabidopsis shade avoidance gene expression in adult plants

Project description:The goal of this study is to obtain genome-wide shade-responsive genes in adult plant. We grew plants under long-day condition with high R/FR ratio (simulated "sun" condition) for two weeks. Plants were treated with shade starting at ZT 4 or left in the sun. We prepared two replicates of each sample at 1 hour and 4 hours after sun and shade treatment and five plants were pooled for each replicate. Cotyledons, hypocotyls, and roots were removed from the samples, leaving leaves and apical tissue.

2015-03-18 | GSE66967 | GEO

Tissue specific light response during Arabidopsis de-etiolation

Project description:The time between seed germination and the development of the first true leaves is crucial for plants success. Depending on the environmental light conditions a plant must decide which developmental program to use. If light is limited, the seedling will use etiolated growth characterized by an elongated hypocotyl and tightly-closed, underdeveloped cotyledons, thus allowing it to reach a light source as quickly as possible. In contrast, seedlings that are grown in unlimited light will use de-etiolation growth, that is characterized by inhibited hypocotyl growth and unhooked, unfolded and fully expanded cotyledons. These seedlings become photosynthetic and increase their chances for reproduction. Interestingly, the outcome of the light signal varies between the seedling’s different organs, e.g. hypocotyl growth is inhibited by light whereas cotyledon expansion is induced. Separating the cotyledons and hypocotyls of de-etiolated seedlings during their first 12 hours of white light exposure, enabled us to perform individual transcriptome analyses of each organ and to examine what causes this variation in light responsiveness.

2020-04-20 | GSE132861 | GEO

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