Project description:Qualitative and quantitative atlas of the transcriptomes, proteomes and phosphoproteomes of 30 tissues of the model plant Arabidopsis. We describe how many genes were detected as proteins (>18,000), where they are expressed, in which approximate quantities (>6 logs dynamic range) and to what extent they are post-translationally modified by phosphorylation (>43,000 sites). We also measured protein complexes in three tissues (flower, root, leaf) using size-exclusion chromatography (SEC-MS) and the seed proteome in response to cycloheximide and MG132 treatment.
Project description:The differentiation of specialized feeding sites in Arabidopsis root cells in response to nematode infestation involves substantial cellular reprogramming of host cells that is not well characterized at the molecular level. Expression data was generated from Arabidopsis root cells undergoing giant cell formation due to nematode infestation and from non-infested control root cells. Cells were laser captured 14 and 21 days after infestation.
Project description:The root epidermis of Arabidopsis provides a simple and experimentally useful model for studying the molecular basis of cell fate and differentiation. The goal of this study was to define the larger gene regulatory network that governs the differentiation of the root hair and non-hair cell types of the Arabidopsis root epidermis. Transcript levels in the root epidermis of wild-type and mutant lines were assessed by purifying populations of root epidermal cells using fluorescence-based cell-sorting. Further, the role of the plant hormones auxin and ethylene on root epidermis development was assessed by defining transcript levels in the root epidermis of plants grown on media containing IAA or ACC. These microarray results were used to construct a comprehensive gene regulatory network that depicts the transcriptional control of root epidermal cell fate and differentiation in Arabidopsis.
Project description:Root branching in response to changes in nitrogen status in the soil, is a dramatic example of the plant’s remarkable developmental plasticity. In recent work we investigated the genetic architecture of developmental plasticity, combining phenoclustering and genome-wide association studies in 96 Arabidopsis thaliana ecotypes with expression profiling in 7 ecotypes, to characterise natural variation in root architectural plasticity at the phenotypic, genetic, and transcriptional levels. This series contains the microarray expression data for 7 ecotypes that represent a range of root branching strategies. We used microarrays to detail the global programme of gene expression involved in the plants response to nitrogen in the root and identified distinct classes of up- and down-regulated genes in the seven different Arabidopsis ecotypes during this process.
Project description:Plant adaptation to limited phosphate (Pi) availability comprises a wide range of strategies to conserve and remobilize internal Pi stores and to enhance Pi acquisition. Vigorous restructuring of root system architecture provides a developmental strategy for topsoil exploration and Pi scavenging. Changes in external Pi availability are locally sensed at the root tip and adjust root growth by modulating cell expansion and cell division. The functionally interacting Arabidopsis genes, LPR1/LPR2 and PDR2, are key components of root Pi sensing. A series of genome-wide studies revealed insight into transcriptional changes upon Pi starvation and provided a comprehensive overview of gene expression patterns in roots and photosynthetic tissues. In this study, we combined genome-wide transcriptome and proteome profiling in Pi-starved roots of wild-type, pdr2 and lpr1lpr2 seedlings. A comparative analysis of the datasets, combined with physiological and cell biological experiments, reveals a network regulating local root Fe uptake, storage and distribution upon Pi limitation. We further highlight expressional changes of several cell wall-modifying enzymes and provide evidence for a dynamic adjustment of the pectin network at sites of local Fe accumulation within the root meristem.