A combination of plasma membrane sterol biosynthesis and autophagy is required for shade-induced hypocotyl elongation
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ABSTRACT:
PROVIDER: PRJNA730903 | ENA |
REPOSITORIES: ENA
Dataset's files
| Action | DRS | |||
|---|---|---|---|---|
| SRR14580112.fastq.gz | Fastqsanger.gz | |||
| SRR14580113.fastq.gz | Fastqsanger.gz | |||
| SRR14580114.fastq.gz | Fastqsanger.gz | |||
| SRR14580115.fastq.gz | Fastqsanger.gz | |||
| SRR14580116.fastq.gz | Fastqsanger.gz |
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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
Project description:Plant growth ultimately depends on fixed carbon, thus the available light for photosynthesis. Due to canopy light absorption properties, vegetative shade combines low blue (LB) light and a low red to far-red ratio (LRFR). In shade-avoiding plants, these two conditions independently trigger growth adaptations to enhance light access. However, how these conditions, differing in light quality and quantity, similarly promote hypocotyl growth remains unknown. Using RNA sequencing we show that these two features of shade trigger different transcriptional reprogramming. LB induces starvation responses, suggesting a switch to a catabolic state. Accordingly, LB promotes autophagy. In contrast, LRFR induced anabolism including expression of sterol biosynthesis genes in hypocotyls in a manner dependent on PHYTOCHROME-INTERACTING FACTORs (PIFs). Genetic analyses show that the combination of sterol biosynthesis and autophagy is essential for hypocotyl growth promotion in vegetative shade. We propose that vegetative shade enhances hypocotyl growth by combining autophagy-mediated recycling and promotion of specific lipid biosynthetic processes.
| S-EPMC9550796 | biostudies-literature
Project description:We show that longer-term inhibition of shade avoidance in Arabidopsis is sustained by ELONGATED HYPOCOTYL 5 (HY5) and HY5 HOMOLOG (HYH) which, together, regulate transcriptional reprogramming of genes involved in hormone signalling and cell wall modification.
2023-06-07 | GSE192469 | GEO
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.
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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
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.
2016-06-10 | GSE83212 | GEO
Project description:Shade avoidance helps plants maximize their access to light for growth under crowding. It is unknown, however, whether a priming shade avoidance mechanism exists that allows plants to respond more effectively to successive shade conditions. Here, we show that the shade-intolerant plant Arabidopsis can remember a first experienced shade event and respond more efficiently to the next event on hypocotyl elongation. The transcriptional regulator PHYTOCHROME-INTERACTING FACTOR 7 (PIF7) and the histone H3K27-demethylase RELATIVE OF EARLY FLOWERING 6 (REF6) were identified as being required for this shade avoidance memory. RNA-sequencing analysis revealed that shade induction of shade memory-related genes was impaired in the pif7 and ref6 mutants. Based on the enrichments of H3K27me3, REF6 and PIF7, we found that priming shade treatment induced PIF7 accumulation, which further recruited REF6 to demethylate H3K27me3 on the chromatin of certain memory-related genes, leading to a state poised for their transcription. Upon the second shade treatment, enhanced shade-mediated induction of these genes resulted in stronger hypocotyl growth responses. We conclude that the transcriptional memory mediated by epigenetic modification plays a key role in the ability of primed plants to remember previously experienced shade and acquire enhanced responses to recurring shade conditions.
2024-07-29 | GSE268785 | GEO
Project description:Shade avoidance syndrome (SAS) commonly occurs in plants sensing shading and the proximity of neighbors, leading to morphological and physiological changes that are detrimental to plant health and consequently crop yield. Controlling SAS could prove beneficial for sustainable agriculture.Here, we performed a phenotype-based chemical screen in Arabidopsis and identified pfifithrin (PFT-α) as a compound that suppresses shade-induced hypocotyl elongation and gene expression. Through genetic, biochemical, and molecular approaches, we demonstrated that PFT-α mimics ethylene by deactivating the ethylene receptor ETR1. This action influences the expression of Phytochrome-Interacting Factors (PIF4 and PIF7) and subsequently inhibits shade-induced hypocotyl elongation. Our findings suggest that PFT-α, acting as a potent ethylene mimic, plays a crucial role in hormone-regulated plant development and holds promise for modulating SAS in agricultural contexts.
2025-07-16 | GSE272795 | GEO
Project description:The size and shape of plant organs are highly responsive to environmental conditions. The plant's embryonic stem, or hypocotyl, displays phenotypic plasticity, in response to light and temperature. The, hypocotyl of shade avoiding species elongate to outcompete neighbouring plants and secure access to sunlight. Similar elongation occurs in high temperature. PHYTOCHROME-INTERACTING FACTORS (PIFs) family transcription are known to be importenet players in these responses. However, it is poorly understood how environmental light and temperature interact to affect plants development. We found that low R/FR combined with warm temperature produces a synergistic hypocotyl growth response that dependent on PIF7 and the hormone auxin. We demonstrate that additional, unknown factor/s must be working downstream of the phyB-PIF-auxin module. As shade responses are known to affect yield, susceptibility to pathogens, and fruit quality in many species, our findings will improve the predictions of how plants will respond to increased ambient temperatures when grown at high density, a condition in which mutual shading occurs.
2022-07-26 | GSE205208 | GEO
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.
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