Chromatin mechanism of DELLA-mediated gene repression and Gibberellin-induced gene activation in rice
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ABSTRACT:
ORGANISM(S): Oryza sativa Japonica Group
PROVIDER: GSE226812 | GEO | 2023/08/11
REPOSITORIES: GEO
Similar Datasets
Project description:Gibberellin (GA) promotes plant growth primarily by triggering degradation of DELLA transcription regulators, yet how DELLA activity is fine-tuned dynamically by phosphorylation independently of proteolysis remains poorly understood. Here we show that the CDK8 kinase module of the Mediator complex attenuates the activity of the Arabidopsis DELLA protein RGA by modulating coactivator recruitment. Using TurboID-based proximity labeling, biochemical and genetic analyses, we identify CDK8 as an in-planta kinase that phosphorylates RGA at Ser170 within its disordered PolyS/T region. This phosphorylation does not affect RGA stability, localization or interactions with transcription factors or histone H2A, but selectively weakens RGA association with the Mediator subunit MED15, thereby reducing DELLA-dependent transcription activation. Consistently, cdk8 mutants show impaired GA responses and delayed developmental phase transitions that are partially rescued by loss of DELLA function. Our findings uncover a phosphorylation-dependent mechanism by which the Mediator kinase module fine-tunes hormone-responsive transcription through selective control of DELLA–coactivator interactions.
2026-09-14 | PXD077697 | Pride
Project description:Many years after the discovery of GID1 as the GA receptor, the belief in the existence of GA-binding protein (GBP) in aleurone cells still persists. Actually, some recent reviews and textbooks still contain information about the possibility of an alternative GA perception mechanism mediated by GBPs. Thus, to finally clarify this issue, we examined the expression of GA-regulated genes using rice embryoless half-seeds of four kinds of GA signaling mutants, each one independently carrying mutated GID1, DELLA, and GA-related F-box, which are all encoded by single genes in rice, allowing for convenient study of the GA perception system. The comprehensive microarray analysis using these rice mutants revealed that all genes tested to be responsive to GA in the wild-type (WT) aleurone cells consistently did not respond to GA in the gid1 or slr1 mutant.
2014-12-19 | GSE64290 | GEO
Project description:DELLA proteins are members of the GRAS-domain family of transcriptional regulators and modulate transcriptional activity through protein-protein interactions with at least 15 different classes of transcription factor. The plant hormone gibberellin (GA) regulates a range of growth and development responses including promoting cell elongation, by triggering the degradation of DELLA proteins. More than 70% of modern wheat (Triticum aestivum L.) varieties carry alleles encoding DELLA proteins that are resistant to GA-mediated degradation. These alleles result in constitutive growth repression in stem tissues and confer a semi-dwarf growth habit associated with improved lodging resistance. However, these alleles also have negative pleiotropic effects such as reduced nitrogen use efficiency and weak early vigour that restrict their utility in some environments. A detailed understanding of the mechanisms by which DELLA proteins regulate growth and development will be necessary to dissect these responses and develop targeted strategies to breed improved crop varieties. We identified the orthologous C2H2 Zinc-finger transcription factors INDETERMINATE DOMAIN 5 (IDD5) in wheat and SEMI-DWARF3 (SDW3) in barley (Hordeum vulgare) as positive regulators of stem and leaf expansion. Both IDD5 and SDW3 physically interact with DELLA proteins and are epistatic to these genes. We propose a mechanism by which IDD proteins integrate GA signals to modulate downstream gene transcriptional activity through a protein complex dual activation and repression activities. Changes in GA biosynthesis gene expression levels suggest that part of this response involves GA homeostasis. Plants carrying null mutations in IDD5 and SDW3 exhibit a GA-insensitive semi-dwarf growth habit comparable to the Rht-D1b ‘Green Revolution’ allele and have potential as novel dwarfing alleles in cereal breeding programmes.
2024-11-30 | GSE282829 | GEO
Project description:Chromatin mechanism of DELLA-mediated gene repression and Gibberellin-induced gene activation in rice
| PRJNA941831 | ENA
Project description:Gibberellins (GAs) regulate multiple aspects of growth and development in flowering plants, primarily through the canonical GID1-DELLA signaling module. Contrary to the prevailing paradigm that all GA responses require GID1, we demonstrated that a rice GID1-like 2 protein (designated GA Receptor 1, GAR1) is a GA receptor that functions independently of GID1. Isothermal titration calorimetry revealed that GAR1 can bind bioactive GAs, and multiple assays confirmed that GAR1 physically interacts with the promoter of GAMYB, a central regulator of GA responses, whereas GID1 does not. Using a transgenic rice line containing the GA biosensor GIBBERELLIN PERCEPTION SENSOR 1 (GPS1), we demonstrated that the subcellular distributions of GAR1 and its homologs GAR3 and GAR4 overlapped with strong GA signals in specific cells of rice leaves, anthers, and filaments. gar1 gar2 double mutants exhibited a semi-dwarf phenotype with slightly shorter anthers, whereas gar3 gar4 mutants displayed normal plant height with elongated filaments; both double mutants showed slightly reduced male fertility. ChIP-seq analyses revealed enrichment of GAR1 at the promoters of MYBs and other GA-responsive genes associated with tiller height and anther development, and RT-qPCR confirmed that height-related genes were downregulated in gar1 gar2 double mutants. Our findings reveal a non-canonical GA signaling pathway mediated by GAR1, providing new mechanistic insights into GA perception and novel targets for biotechnological manipulation.
2026-08-07 | GSE331473 | GEO
Project description:Many years after the discovery of GID1 as the GA receptor, the belief in the existence of GA-binding protein (GBP) in aleurone cells still persists. Actually, some recent reviews and textbooks still contain information about the possibility of an alternative GA perception mechanism mediated by GBPs. Thus, to finally clarify this issue, we examined the expression of GA-regulated genes using rice embryoless half-seeds of four kinds of GA signaling mutants, each one independently carrying mutated GID1, DELLA, and GA-related F-box, which are all encoded by single genes in rice, allowing for convenient study of the GA perception system. The comprehensive microarray analysis using these rice mutants revealed that all genes tested to be responsive to GA in the wild-type (WT) aleurone cells consistently did not respond to GA in the gid1 or slr1 mutant. All microarray experiments were performed according to the manufacturerM-bM-^@M-^Ys manual. The Feature Extraction software (Agilent Technologies) was used to delineate and measure the Cy3 and Cy5 signal intensities of each spot in the array. The resulting data were normalized using the Variance-stabilizing normalization (VSN) algorithm.
2014-12-19 | E-GEOD-64290 | biostudies-arrayexpress
Project description:DELLA proteins act as transcription regulators that repress gibberellin (GA) responses and are best known for controlling the semi-dwarf crop varieties that drove the Green Revolution. DELLAs regulate gene expression primarily through protein–protein interactions with transcription factors and chromatin regulators. Recent work further indicates that DELLA activity involves formation of transcription factor–DELLA–histone H2A complexes at target loci and recruitment of the Mediator coactivator complex via the tail subunit MED15. Although DELLAs are known phosphoproteins, the kinases responsible and the functional significance of DELLA phosphorylation—particularly independent of GA‑induced proteolysis—remain unknown. To identify kinase(s) that associate with the Arabidopsis DELLA protein RGA in planta, we performed TurboID (TbID) proximity labeling to capture target proteins such as protein kinases that may only transiently interact with RGA in planta. RGA proximitome includes the CDK8 kinase module of the Mediator complex and a broad set of DELLA-associated transcription regulators.
2026-07-28 | PXD078134 | Pride
Project description:The goal of this study was to search for DELLA-independent GA-regulated genes in tomato. RNA deep sequencing (RNA-seq) was performed to GA-treated M82 and pro∆GRAS mutant. Using a two fold increased or decreased cutoff we identified 81 GA-up regulated and 15 GA-down regulated genes, from which five genes were DELLA-independent.
2015-07-09 | GSE68018 | GEO
Project description:The aim of this study is to identify early DELLA protein-responsive genes using a Dexamethasone (DEX)-inducible system. Two transgenic lines were used: one induces the expression of a dominant, gibberellin non-responsive DELLA protein (rga-delta17); the other is a control line that carries the same vector, but lacks the rga-delta17 transgene. By comparing the gene expression changes in the line that expresses the rga-delta17 protein in the presence or absence of DEX it is possible to identify putative targets of DELLA proteins. An empty vector transgenic line was included in this study to identify genes that might be regulated by the DEX inducible system that are not dependent on the DELLA protein. Experiment Overall Design: Seedlings of both transgenic lines were pretreated for 16 h with 2 uM GA4 to enhance gibberellin responses. Because DELLA proteins are strong signaling repressors, this pretreatment should maximize the effect of DELLA induction. Eight-day old seedlings were treated with 2 uM GA4 or a combination of 2 uM GA4 plus 10 uM DEX to induce the rga-delta17 transgene. Three biological replicas for the transgenic line that carries the DEX-inducible rga-delta17 transgene were generated at 2h and 4h. For the empty vector line, only 2 biological replicas were generated at 4h of treatment with 2 uM GA with or without 10 uM DEX.
2008-06-16 | E-GEOD-8741 | biostudies-arrayexpress
Project description:Brassinosteroid (BR) and gibberellin (GA) promote many similar developmental responses in plants; but their relationship remains unclear. Here we show that BR and GA act interdependently through a direct interaction between the BR-activated BZR1 and GAinactivated DELLA transcription regulators. GA promotion of cell elongation required BR signaling, whereas BR or active BZR1 can suppresssed the GA-deficient dwarf phenotype. DELLAs directly interacted with BZR1 and inhibited BZR1-DNA binding both in vitro and in vivo. Genome-wide analysis defined a BZR1-dependent GA-regulated transcriptome, which is enriched with light-regulated genes and genes involved in cell wall synthesis and photosynthesis/chloroplast. GA promotion of hypocotyl elongation requires both BZR1 and the phytochrome interacting factors (PIFs), as well as their common downstream targets PREs. The results demonstrate that GA releases DELLA-mediated inhibition of BZR1, and that the DELLA-BZR1-PIF4 interaction defines a core transcription module that mediates coordinated growth regulation by GA, BR and light signals.
2012-06-25 | GSE35408 | GEO