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Profiling primary downstream target of LBD16 in roots of Arabidopsis thaliana

ABSTRACT: Lateral roots (LRs) are formed post-embryonically and contribute to root architecture formation in vascular plants. LATERAL ORGAN BOUNDARIES-DOMAIN 16 (LBD16) is a key transcription factor to initiate LR formation functioning redundantly with related LBD members. To identify primary downstream targets of LBD16, we engineered a transgenic line with inducible LBD16 activity by expressing a fusion protein of LBD16 and rat glucocorticoid receptor (GR) under the regulation of its own regulatory region (gLBD16-GR) in the lbd16-1 lbd18-1 lbd33-1 mutant. Here we identified primary response genes of LBD16 from transcriptome analysis.

ORGANISM(S): Arabidopsis thaliana

PROVIDER: GSE115420 | GEO | 2018/12/31

REPOSITORIES: GEO

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Gene expression analysis of Arabidopsis root in LBD16-GR overexpression line

Project description:Lateral roots (LRs) are formed post-embryonically and contribute to root architecture formation in vascular plants. LATERAL ORGAN BOUNDARIES-DOMAIN 16 (LBD16) is a key transcription factor to initiate LR formation. LBD16 functions downstream of AUXIN RESPONSE FACTOR 7 (ARF7) and ARF19, and overexpression of LBD16 partially restores LR formation in the absence of ARF7 and ARF19. To identify downstream targets of LBD16, we engineered a transgenic line with inducible LBD16 activity by overexpressing a fusion protein of LBD16 and rat glucocorticoid receptor (GR) in arf7 arf19 mutant. Here we identified primary response genes of LBD16 from transcriptome analysis of 35Spro:LBD16:GR arf7 arf19 line.

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Transcription profiling by array of Arabidopsis overexpressing LBD16 and LBD18 to investigate downstream genes

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2011-06-01 | E-MEXP-1400 | biostudies-arrayexpress

Total expression profiling of embryonic regions of EHF mouse embryos

Project description:Establishment of left-right (LR) asymmetry occurs shortly after gastrulation and utilizes a cascade of events. In the mouse, LR symmetry is broken at the node, involves signal relay to the lateral plate, and results in asymmetric organ morphogenesis. How information transmits from the node to the lateral plate remains unclear. Noting that embryos lacking Sox17 exhibit defects in both gut endoderm formation and LR patterning, we investigated a connection between these two processes. We noted an endoderm-specific absence of the critical gap junction component, Connexin43, in Sox17 mutants. Dye-coupling experiments revealed planar gap junction coupling across the gut endoderm in wild-type but not mutant embryos. The role for gap junction communication in LR patterning was confirmed by pharmacological inhibition. Collectively, our data demonstrate communication across gap junctions in gut endoderm as a mechanism for information relay between node and lateral plate critical for the establishment of LR asymmetry in mice. Total RNA isolated from embryonic regions of wild-type embryos at EHF stages, three samples per well, in triplicates

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The multivalency of the glucocorticoid receptor ligand-binding domain explains its manifold physiological activities

Project description:The glucocorticoid receptor (GR) is a ubiquitously expressed transcription factor that controls metabolic and homeostatic processes essential for life. Although numerous crystal structures of the GR ligand-binding domain (GR-LBD) have been reported, the functional oligomeric state of the full-length receptor (FL-GR), which is essential for its transcriptional activity, remains disputed. Here we present five new crystal structures of agonist-bound GR-LBD, along with a thorough analysis of previous structural work. We identify four distinct homodimerization interfaces on the GR-LBD surface, which can associate into 20 topologically different homodimers. Biologically relevant homodimers were identified by studying a battery of GR point mutants including crosslinking assays in solution, quantitative fluorescence microscopy in living cells, and transcriptomic analyses. Our results highlight the relevance of non-canonical dimerization modes for GR, especially of contacts made by loop L1-3 residues such as Tyr545. Our work illustrates the unique flexibility of GR’s LBD and suggest many dimeric conformations can coexist within cells. In addition, we unveil pathophysiologically relevant quaternary assemblies of the receptor with important implications for glucocorticoid action and drug design.

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Total expression profiling of embryonic regions of EHF mouse embryos

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Project description:Isoprene is a C5 volatile organic compound, which can protect aboveground plant tissue from abiotic stress such as short-term high temperatures and accumulation of reactive oxygen species (ROS). Here, we uncover new roles for isoprene in the plant belowground tissues. By analyzing Populus x canescens isoprene synthase (PcISPS) promoter reporter plants, we discovered PcISPS promoter activity in certain regions of the roots including the vascular tissue, the differentiation zone and the root cap. Treatment of roots with auxin or salt increased PcISPS promoter activity at these sites, especially in the developing lateral roots (LR). Transgenic, isoprene non-emitting poplar roots revealed an accumulation of O2 - in the same root regions where PcISPS promoter activity was localized. Absence of isoprene emission, moreover, increased the formation of LRs. Inhibition of NAD(P)H oxidase activity suppressed LR development, suggesting the involvement of ROS in this process. The analysis of the fine root proteome revealed a constitutive shift in the amount of several redox balance, signaling and development related proteins, such as superoxide dismutase, various peroxidases and linoleate 9S-lipoxygenase, in isoprene non-emitting poplar roots. Together our results indicate for isoprene a ROS-related function, eventually co-regulating the plant-internal signaling network and development processes in root tissue. This article is protected by copyright. All rights reserved.

2020-06-16 | PXD019789 | Pride

The multivalency of the glucocorticoid receptor ligand-binding domain explains its manifold physiological activities

Project description:The glucocorticoid receptor (GR) is a ubiquitously expressed transcription factor that controls metabolic and homeostatic processes essential for life. Although numerous crystal structures of the GR ligand-binding domain (GR-LBD) have been reported, the functional oligomeric state of the full-length receptor, which is essential for its transcriptional activity, remains disputed. Here we present five new crystal structures of agonist-bound GR-LBD, along with a thorough analysis of previous structural work. Biologically relevant homodimers were identified by studying a battery of GR point mutants including crosslinking assays in solution and quantitative fluorescence microscopy in live cells. Our results highlight the relevance of non-canonical dimerization modes for GR, especially of contacts made by loop L1-3 residues such as Tyr545. Our work unveils likely pathophysiologically relevant quaternary assemblies of the nuclear receptor with important implications for glucocorticoid action and drug design.

2023-03-11 | PXD028039 | Pride

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