E-GEOD-27077
Ontology highlight
ABSTRACT:
OTHER RELATED OMICS DATASETS IN: PRJNA137539
PROVIDER: E-GEOD-27077 | ExpressionAtlas | 2015-12-03
REPOSITORIES: ExpressionAtlas
Dataset's files
| Action | DRS | |||
|---|---|---|---|---|
| E-GEOD-27077-analysis-methods.tsv | Tabular | |||
| E-GEOD-27077-atlasExperimentSummary.Rdata | Rdata | |||
| E-GEOD-27077-configuration.xml | Xml | |||
| E-GEOD-27077-percentile-ranks.tsv | Tabular | |||
| E-GEOD-27077.condensed-sdrf.tsv | Tabular |
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Project description:The main purpose of this work is to clarify the effect of bacterial PLR on lateral root development in Arabidopsis, especially focusing on the fluctuation of auxin signaling in plants, so as to explain that PLR promotes lateral root development by promoting auxin signaling in plants.
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Project description:The phytohormone auxin controls a myriad of processes in plants, at least in part through its regulation of cell expansion. The "acid growth hypothesis" has been proposed to explain auxin-stimulated cell expansion for five decades, but the mechanism underlying auxin-induced cell wall acidification is poorly characterized. Auxin induces the phosphorylation and activation of the plasma membrane (PM) H+-ATPase that pumps protons into the apoplast, yet how auxin activates its phosphorylation remains elusive. Here, we show that the transmembrane kinase (TMK) auxin signaling proteins interact with PM H+-ATPases and activate their phosphorylation to promote cell wall acidification and hypocotyl cell elongation in Arabidopsis. Auxin induced TMK's interaction with H+-ATPase on the plasma membrane within 1-2 minutes as well as TMK-dependent phosphorylation of the penultimate Thr residue. Genetic, biochemical, and molecular evidence demonstrates that TMKs directly phosphorylate PM H+-ATPase and are required for auxin-induced PM H+-ATPase activation, apoplastic acidification, and cell expansion. Thus, our findings reveal a crucial connection between auxin and PM H+-ATPase activation in regulating apoplastic pH changes and cell expansion via TMK-based cell surface auxin signaling.
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Project description:The plant signaling molecule auxin triggers both fast and slow cellular responses across the plant lineage, including both land plants and algae. We discovered an ultra-fast proteome-wide phosphorylation response to auxin across 5 land plant and algal species, converging on a core group of shared target proteins. We find conserved rapid physiological responses to auxin in the same species and identified a RAF-like protein kinase as a central mediator of auxin-triggered phosphorylation across species.
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Project description:KNOTTED1(KN1)-like homeobox (KNOX) transcription factors function in plant meristems, self-renewing structures consisting of stem cells and their immediate daughters. Despite their importance for plant development, the genomic network targeted by KNOX proteins is poorly understood. Using ChIP-seq, we defined the KN1 cistrome in maize inflorescences and found that KN1 binds to several thousand loci. To understand how these binding occupancies correlate with changes in transcriptional regulation, we performed RNA-seq on immature ears and tassels, and compared expression profiles between normal and loss-of-function kn1 plants, in addition to immature leaves from normal and gain-of-function Kn1 plants. We found that 643 of the KN1 targets were modulated in one or multiple tissues, with a strong enrichment for transcription factors (including other homeobox genes) and genes participating in several hormonal pathways, most significantly auxin, implicating KN1 at the crossroads of plant hormone signaling. The loss-of-function kn1 phenotype is reminiscent of auxin mutants and kn1 mis-expression in leaves correlates with increased auxin signaling. Our results demonstrate that KN1 plays a key role in orchestrating the upper levels of a hierarchical gene regulatory network that impacts plant meristem identity and function. ChIP-seq was performed using ear primordia and tassel primordia. Input DNA from each sample was used as a normalization control
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Project description:Auxin plays diverse and profound roles in plants, regulating essentially all aspects of plant growth and development. Yet how auxin achieves such functional diversity and specificity is largely unknown. Here, we address how different concentrations of auxin determine developmental responses through auxin signaling pathways, which are essential for differential growth including apical hook development. We showed that a high auxin concentration at concave side of the apical hook stimulated the C-terminus cleavage and cytosolic translocation of Transmembrane Kinase 1 (TMK1), which then phosphorylates non-canonical IAA32 and IAA34. Surprisingly, and in contrast to the previous report that auxin degrades IAA proteins through the TIR1/AFB auxin receptor to regulate gene expression, here we found that non-canonical IAA32 and IAA34 proteins were stabilized by the high auxin concentration through TMK1 cleavage to negatively regulate gene expression and inhibit growth. Thus, we demonstrated that TIR1/AFB-independent transcriptional auxin signaling regulated growth inhibition in response to the high auxin concentration.
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Project description:Proper functioning of the nuclear auxin pathway is essential for regulating plant growth and development by maintaining auxin homeostasis. To understand better physiological mechanisms involved in auxin signaling pathways we investigated the localization and effect of accumulation of auxin coreceptor IAA17/AXR3 in root. We demonstrate that the accumulation of stable nuclear AXR3-1 protein interferes with auxin homeostasis, causing auxin insensitivity and increased rapid root cell elongation followed by detained growth. This growth pattern is associated with changes in phytohormone gene expression. Data from transcriptomic screen combined with reporter lines and mutant studies declare essential role of auxin homeostasis in maintaining optimal root growth rate and development. We proposed a model in which rapid cell elongation is caused by combination of AXR3-1-dependent auxin insensitivity associated with unblocked gibberellin effect on root. This study demonstrate that plants coordinate gibberellin homeostasis by the auxin signaling pathway, contributing to avoid excessive root elongation.
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Project description:Auxin is essential for plant growth and development by altering downstream gene expression. Although large progresses have been made on auxin-concentration, distribution and signaling pathways in model plants like Arabidopsis and rice, little is known in moso bamboo which belongs to grass family, and has great economic and social value. Here we performed genome-wide analysis of the key components related to auxin action, and identified 13 YUCCA genes for auxin synthesis, 14 PIN-FORMED/PIN-like (PIN/PILS) proteins 7 AUXIN1/LIKE-AUX1 (AUX1/LAX) family members for auxin transport, 10 auxin binding factors (AFB) for auxin perception, 43 auxin/indole-3-aceticacid (AUX/IAA) and 41 auxin response transcription factors (ARF) genes for auxin signaling in moso bamboo genome. We further performed phylogenetic analysis of those auxin action related genes from Arabidopsis, Oryza sativa and moso bamboo. To know those genes’ ability to response exogenous auxin and to generate a comprehensive transcriptome overview of auxin response in moso Bamboo, we performed RNA_seq analysis. Our data showed that auxin regulates genes related its biosynthesis, transport, signaling. Moreover, we present the interaction between auxin and other phytohormones at the level of transcription. In summary, we identified the key gene families involved in the auxin action pathways in moso bamboo, and generated a transcriptional overview of the auxin response in moso bamboo. Our data open up an opportunity to uncover the precise roles of auxin action pathways in this important species.
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