Transcription profiling of Lycopersicon esculentum roots in wild-type and ABA-deficient, control and Glomus intraradices inoculated plants to characterise variations in mycorrhization.
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ABSTRACT: Abscisic acid (ABA) determines mycorrhiza functionality and arbuscule development. Transcriptome analysis in response to different mycorrhization status according to the ABA concentration in the root was performed to identify genes that may play a role in arbuscule functionality. Tomato Affymetrix GeneChip (around 10,000 probes) allowed us to detect and compare the transcriptional root profiling of tomato (Solanum lycopersicum) wild-type and ABA-deficient sitiens plants colonized by the arbuscular mycorrhizal fungus Glomus intraradices.
Project description:The transcriptome profile of arbuscular mycorrhiza established at 4 weeks post inoculation between Medicago truncatula and Glomus mosseae as well as between Medicago truncatula and Glomus intraradices is compared
Project description:Detailed information: Rice (*Oryza sativa* L. cv. Nipponbare) is a drought-susceptible species which is well suited for studies of abiotic stress response because of the comprehensive bioinformatics resource available. By withholding water from the entire root system of young rice plants, or half the root system only, it was possible to infer the relative impact of signals arriving from roots growing in wet and dry soil on the shoot proteome. The global proteome of shoots had 685 proteins in common to all three drought treatments but there were major shifts in abundance of individual proteins within 16 functional categories. The dominant changes were analyzed more deeply. First, we investigated transport and cell component organization, where some proteins were up-regulated by drought but many more down-regulated. Proteins involved in protein metabolism were up-regulated in general by drought when they were responsible for protein degradation but those involved in protein synthesis were down-regulated when water was withheld. Stress-related proteins behaved very consistently by increasing in droughted plants but notably some proteins were most abundant when roots of the same plant were growing in both wet and dry soil. This suggests that drought signals are complex interactions and not simply the additive effect of water supply to the roots. Changes in carbohydrate-processing proteins were consistent with the passive accumulation of soluble sugars in shoots under drought, with hydrolysis of sucrose and starch synthesis both enhanced. Data analysis information: The result raw files were converted to mzXML format and processed through the global proteome machine (GPM) software (version 2.1.1) of the X!Tandem algorithm (freely available at http://www.thegpm.org). The 16 gel fractions were processed serially for each experiment and the output files were generated as non-redundant, merged files with protein identifications with log (e) values less than -1, for each individual gel fraction. A protein database compiled from NCBI *O*. *sativa* with 26938 protein sequences (August 2011) was used in GPM to search the tandem mass spectra; the database also included common trypsin and human peptide contaminants. False discovery rates (FDR) were evaluated by searching against a reversed sequence database. Search parameters included MS and MS/MS tolerances of +2 Da and +0.2 Da, carbamidomethylation of cysteine as fixed modifications, oxidation of methionine as variable modifications and tolerance of two missed tryptic cleavages and K/R-P cleavages.
Project description:Lotus japonicus is a perennial legume with a small diploid genome that has been adopted as a model species for legume genetics and genomics. With the genome sequence as a backdrop (Sato et al. 2008), we have generated a gene expression atlas that provides a global view of gene expression in all major organ systems of this species, including nodule and seed development.
Project description:Trees establish a symbiotic relationship with specialized soil fungi, called ectomycorrhizae, which is essential for nutrition, growth and health of temperate forest ecosystems. Understanding the mechanisms governing the establishment and functioning of ectomycorrhiza is important because of the role of forests in sequestering CO2 and also to develop ways to optimize tree productivity and sustainability. Here, we investigated the response of an oak species to ectomycorrhiza formation using a two dimensional differential in gel electrophoresis (2D-DIGE) and MALDI-TOF/TOF mass spectrometry proteomics approach. At the root level, changes in the abundance of 34 unique oak proteins were detected and revealed proteins involved in carbon and energy metabolism, protein processing and degradation, response to oxidative stress, lipid metabolism/transport, nitrogen and phosphorous assimilation and cell wall modification. Proteins supporting the importance of the secretory pathway functioning, in particular of the endoplasmic reticulum, during ectomycorrhiza functioning were identified. These proteins were identified as components of the endoplasmic reticulum folding/chaperoning machinery and proteins involved in the ER quality control system. This study constitutes an important contribution for the understanding of the mechanisms underlying the response of plants to ectomycorrhizal symbiosis establishment.
Project description:Two alfalfa varieties, 'Chilean' (M. sativa ssp. sativa var. Chilean, drought sensitive) and 'Wisfal' (M. sativa ssp. falcata var. Wisfal, drought tolerant), with contrasting water use efficiency were subjected to water withholding for 11 days followed by re-watering. Samples were taken for well-watered plants and plants after five, eight, eleven days of drought stress as well as plants after recovery for one day following drought stress. Roots and shoots were sampled and analyzed separately by expression profiling using Affymetrix Medicago GeneChip.
Project description:Xanthomonas oryzae pv. oryzae (Xoo), the causative agent of bacterial blight disease, is one of the major threats to rice productivity. Yet, the molecular mechanism of rice-Xoo interaction is elusive. Here, we report comparative proteome profiles of Xoo susceptible (Dongjin) and resistant (Hwayeong) cultivars of rice in response to two-time points (3 and 6 days) of Xoo infection. Low-abundance proteins were enriched using a protamine sulfate (PS) precipitation method and isolated proteins were quantified by a label-free quantitative analysis, leading to the identification of 3846 protein groups. Of these, 1128 proteins were significantly changed between mock and Xoo infected plants of Dongjin and Hwayeong cultivars. Based on the abundance pattern and functions of the identified proteins, a total of 23 candidate proteins were shortlisted that potentially participate in plant defense against Xoo in the resistant cultivar. Of these candidate proteins, a mitochondrial arginase-1 showed Hwayeong specific abundance and was significantly accumulated following Xoo inoculation. Overexpression of arginase-1 in susceptible rice cultivar (Dongjin) resulted in enhanced tolerance against Xoo as compared to the wild-type (WT). In addition, expression analysis of defense-related genes encoding PR1, glucanase I, and chitinase II by qRT-PCR showed their enhanced expression in the overexpression lines as compared to WT. Mitochondrial localization of the selected arginase was further confirmed by fluorescent microscopy using GFP-tagged arginase. Taken together, our results uncover the proteome changes in the rice cultivars and highlight the functions of arginase in plant defense against Xoo.
Project description:cortical cell of non-mycorrhizal roots (cor), arbuscule-containing cells (arb) and non-arbuscule-containing cells (nac) of M. truncatula roots colonized with Glomus intraradices were collected by laser capture microdissection (LCM) and used for RNA extraction and Medicago microarray hybridisation
Project description:Ozone at an elevated level is an important environmental stress factor that limits plant growth and development. To test how O3-induced ROS signalling interacts with the ABA pathway we present a global characterization of O3-responsive genes in the abi1td mutant. To understand better ABA signalling and the interactions between stress-response pathways we also performed a microarray analysis of drought-treated abi1td and WT plants. Since ABA signalling is well known to mediate defined responses based on the WT and different mutants analysis in drought stress conditions, the comparison of the O3 and drought stress response in abi1td enabled the identification of new processes depending on ABA-related pathways in O3-treated plants. Altogether, our findings indicate that ABI1 plays the role of a general signal transducer linking diferrent hormone signalling pathways to O3 stress tolerance.<br><br><br><br>Key words: ROS signalling; ABA signalling; ozone stress; drought stress; environmental stress; gene knockout;
Project description:To dissect differences in gene expression profile of soybean roots inoculated with wild-type and type III secretion mutant rhizobia, we have employed microarray analysis. Seeds of soybeans (Glycine max L. cv. Enrei and its non-nodulating line En1282) were surface-sterilized and germinated at 25 M-BM-0C for 2 days and were transferred to a plant box (CUL-JAR300; Iwaki, Tokyo, Japan) containing sterile vermiculite watered with B&D nitrogen-free medium (Broughton and Dilworth 1971). One day after transplant, each seedling was inoculated with Bradyrhizobium elkanii USDA61, its type III secretion mutant BerhcJ or sterilized water (mock treatment). Plants were cultivated in a growth chamber at 25M-BM-0C and 70% humidity with a daytime of 16 h followed by a nighttime of 8 h. To determine the gene expression, RNA was extracted from the roots 8 days after inoculation. Gene expression in soybean roots inoculated with Bradyrhizobium elkanii USDA61, its type III secretion mutant BerhcJ or sterilized water (mock treatment) was measured 8 days after inoculation. Three independent experiments were performed at each inoculation.
Project description:To identify host signaling pathways triggered by P. omnivora<br>infection, we used microarrays to monitor the expression profiles<br>and the molecular process associated with initial entry at 3 days post-inoculation and colonization at 5 days post-inoculation