TOR acts as metabolic gatekeeper for auxin-dependent lateral root initiation in Arabidopsis thaliana
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ABSTRACT:
PROVIDER: PRJNA818896 | ENA |
REPOSITORIES: ENA
Similar Datasets
Project description:To get a genome wide picture of the effects of TOR knockdown during the early phase of lateral root formation, we compared by RNA-seq the transcriptomes of roots 6h after the synchronous induction of lateral formation by auxin treatment (Himanen et al, 2002 - http://dx.doi.org/10.1105/tpc.004960) in the inducible UB10pro>>amiR-TOR background.
2022-03-23 | GSE199202 | GEO
Project description: Not available
| S-SCDT-10_15252-EMBJ_2022111273 | biostudies-other
Project description:This SuperSeries is composed of the SubSeries listed below. https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE199202 https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE199203
2022-03-23 | GSE199211 | GEO
Project description:Lateral root initiation was used as a model system to study the mechanisms behind auxin-induced cell division. Genome-wide transcriptional changes were monitored during the early steps of lateral root initiation. Inclusion of the dominant auxin signaling mutant solitary root1 (slr1) identified genes involved in lateral root initiation that act downstream of the AUX/IAA signaling pathway. Interestingly, key components of the cell cycle machinery were strongly defective in slr1, suggesting a direct link between AUX/IAA signaling and core cell cycle regulation. However, induction of the cell cycle in the mutant background by overexpression of the D-type cyclin (CYCD3;1) was able to trigger complete rounds of cell division in the pericycle that did not result in lateral root formation. Therefore, lateral root initiation can only take place when cell cycle activation is accompanied by cell fate respecification of pericycle cells. The microarray data also yielded evidence for the existence of both negative and positive feedback mechanisms that regulate auxin homeostasis and signal transduction in the pericycle, thereby fine-tuning the process of lateral root initiation. Keywords: time-course wild type vs mutant comparison
2005-11-01 | GSE3350 | GEO
Project description:We performed targeted purification of polysomal mRNA (TRAP-Seq, Vragović et al, 2015 - http://dx.doi.org/10.1073/pnas.1417947112) using a transgenic line ubiquitously expressing a GFP-tagged RPL18 (Mustroph et al, 2009 - https://doi.org/10.1073/pnas.0906131106) 6h after the synchronous induction of lateral root formation by auxin treatment (IAA) upon inhibition of TOR activity (AZD8055 treatment, AZD). To correct for abundance of mRNA, bulk RNA-Seq was performed on the same samples and used to normalise the reads purified with the ribosomes.
2022-03-23 | GSE199203 | GEO
Project description:Genome wide transcriptome profiling of pericycle cells from roots exposed to auxin, cytokinin and both hormones simultaneously. Lateral root organogenesis in Arabidopsis is governed by a complex network of hormonal regulations. Plant hormones auxin and cytokinin were demonstrated to be the key regulators of this lateral root organogenesis and their mode of interaction is antagonistic. The aim of the project is to understand the role of the auxin - cytokinin signalling pathways in lateral root organogenesis.
2020-03-13 | GSE146778 | GEO
Project description:Protein phosphorylation is instrumental to early signaling events. Studying system-wide phosphorylation in relation to processes under investigation requires a quantitative proteomics approach. In Arabidopsis, auxin application can induce pericycle cell divisions and lateral root formation. Initiation of lateral root formation requires transcriptional reprogramming following auxin-mediated degradation of transcriptional repressors. The immediate early signaling events prior this derepression are virtually uncharacterized. To identify the signal molecules responding to auxin application we used the Lateral Root Inducible System which was previously developed to trigger synchronous division of pericycle cells. To identify and quantify the early signaling events following this induction we combined 15N based metabolic labeling and phospho-enrichment and applied a mass spectrometry based approach. In total, 3068 phosphopeptides were identified from auxin treated root tissue. This experiment represents one of the largest quantitative phosphoprotein dataset on Arabidopsis to date. Key proteins responding to auxin treatment included the MDR and PIN2 auxin carriers, auxin response factor2, suppressor of auxin resistance3 and sorting nexin1 (SNX1). Mutational analysis of Serine16 of SNX1 showed that overexpression of the mutated forms of SNX1led to retarded growth and reduction of lateral root formation due to the reduced outgrowth of the primodium, showing proof of principle for our approach. Data Processing: All MS/MS spectra were centroided and merged to a single peak list file using MaxQuant (version 1.0.13.13), which was searched using the Mascot search engine (version 2.2.0, Matrix Science) containing a total 67344 entries (which includes contaminants and an equivalent number of decoy sequences) generated from the publicly available Arabidopsis database (The Arabidopsis Information Resource (TAIR9); June 2009; file name, TAIR9_pep_20090619) with carbamidomethylcysteine as a fixed modification. Oxidized methionine and phosphorylation (serine, threonine, and tyrosine) were searched as variable modifications. Searches were done with tryptic specificity allowing two miscleavages and an initial tolerance on mass measurement of 50 ppm in MS mode and 0.6 Da for MS/MS ions and score cutoff of 20. The resulting .dat files were exported and filtered for a <1% false discovery rate (FDR) at the peptide level using in-house developed software Rockerbox (Version1.1.0) (35). Relative quantification ratios of the identified phosphopeptides and protein were derived by MSQuant (MSQ2.0b4, 2010-02-25) (36). Proteins were quantified with at least two unique non phosphopeptides or single peptide with a score no less than 60. The phospho peptide ratio was normalized by dividing the ratio of its protein of origin. To determine whether phosphorylation ratios for normalized peptides were significantly different a p-value was generated using significance B which is part of the MaxQuant package. The changes were considered significant at a p-value of 0.05 or less. For comparison at the phosphopeptide level the most recent the full dataset with experimental sites was downloaded from PhosPhAt 4.0. Phosphopeptides with ambiguous residues denoted as (s), (t), etc., were converted to S and T, respectively. In addition we used Supplementary Table S1 from Lan et al., (2012) for phosphopeptide comparison. Modifications other than nonambiguous phosphorylation were ignored resulting in a reduction from the original 879 phosphopeptides to 556 peptides. We used pep2pro 'TAIR10 wos' dataset for comparison at the protein level.
2014-02-25 | PXD000177 | Pride
Project description:In maize, nitrate regulates root development thanks to the coordinated action of many players. In this study, the involvement of SLs and auxin as putative downstream components of the nitrate regulation of lateral root development was investigated. To this aim, the endogenous SL content of maize root in response to nitrate availability was assessed by means of LC-MS/MS and measurements of lateral root density in the presence of analogues or inhibitors of auxin and strigolactones were performed. Furthermore, un untargeted RNA-seq based approach was used to better characterize the participation of auxin and strigolacotones to the transcriptional signature of maize root response to nitrate. Our results suggested that N deprivation toughly induces zealactone and carlactonoic acid biosynthesis in maize root, to a higher extent if compared to P-deprived roots. Moreover, data on lateral root density led to hypothesise the existence of both auxin-dependent and auxin-independent effects of nitrate on LR development. In addition, the inhibition of SL biosynthesis seems to participate to the auxin-dependent induction of LR, but the involvement of further downstream unknown components cannot be ruled out.
2021-04-11 | GSE162411 | GEO
Project description:Lateral root initiation was used as a model system to study the mechanisms behind auxin-induced cell division. Genome-wide transcriptional changes were monitored during the early steps of lateral root initiation. Inclusion of the dominant auxin signaling mutant solitary root1 (slr1) identified genes involved in lateral root initiation that act downstream of the AUX/IAA signaling pathway. Interestingly, key components of the cell cycle machinery were strongly defective in slr1, suggesting a direct link between AUX/IAA signaling and core cell cycle regulation. However, induction of the cell cycle in the mutant background by overexpression of the D-type cyclin (CYCD3;1) was able to trigger complete rounds of cell division in the pericycle that did not result in lateral root formation. Therefore, lateral root initiation can only take place when cell cycle activation is accompanied by cell fate respecification of pericycle cells. The microarray data also yielded evidence for the existence of both negative and positive feedback mechanisms that regulate auxin homeostasis and signal transduction in the pericycle, thereby fine-tuning the process of lateral root initiation. Experiment Overall Design: Seedlings of both wild type (Col-0) and the lateral root defective mutant (slr-1) were germinated on MS medium supplemented with 10μM NPA (=auxin transport inhibitor). Three days after germination, such seedlings were transferred to MS supplemented with 10μM NAA for 0h, 2h and 6h respectively. The segment between root meristem and root-hypocotyl junction was harvested from about 1500 seedling per time point. All treatments were repeated biologically. 5.8 μg total RNA was used for the preparation of biotinylated cRNA. Labeled RNA was hybridised to ATH1 Affymetrix chips. The resulting data was MAS5.0 normalised.
2007-07-13 | E-GEOD-3350 | biostudies-arrayexpress
Project description:The acquisition of water and nutrients by plant roots is a fundamental aspect of agriculture and strongly depends on root architecture. Root branching and expansion of the root system is achieved through the development of lateral roots and is to a large extent controlled by the plant hormone auxin. However, the pleiotropic effects of auxin or auxin-like molecules on root systems complicate the study of lateral root development. Here we describe a small-molecule screen in Arabidopsis thaliana that identified naxillin as what is to our knowledge the first non-auxin-like molecule that promotes root branching. By using naxillin as a chemical tool, we identified a new function for root cap-specific conversion of the auxin precursor indole-3-butyric acid into the active auxin indole-3-acetic acid and uncovered the involvement of the root cap in root branching. Delivery of an auxin precursor in peripheral tissues such as the root cap might represent an important mechanism shaping root architecture. To further explore the specificity of naxillin for lateral root development, we compared the early effects of naxillin at the transcriptome level with NAA (1-Naphthaleneacetic acid) in roots of 3-day-old seedlings after 2-h and 6-h treatment.
2012-12-18 | GSE42896 | GEO