Nar nodule vs root transcriptome-analysis of symbiotic root nodule development
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ABSTRACT:
ORGANISM(S): Medicago sativa Medicago truncatula
PROVIDER: GSE121571 | GEO | 2018/11/01
REPOSITORIES: GEO
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Project description:nar nodule vs root transcriptome-analysis of symbiotic root nodule development
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Project description:Alkaline salts (e.g., NaHCO3 and Na2CO3) causes more severe morphological and physiological damage to plants than neutral salts (e.g., NaCl and Na2SO4) due to differences in pH. The mechanism by which plants respond to alkali stress is not fully understood, especially in plants having symbotic relationships such as alfalfa (Medicago sativa L.). Therefore, a study was designed to evaluate the metabolic response of the root-nodule symbiosis in alfalfa under alkali stress using comparative metabolomics. Rhizobium-nodulized (RI group) and non-nodulized (NI group) alfalfa roots were treated with 200 mmol/L NaHCO3 and, roots samples were analyzed for malondialdehydyde (MDA), proline, glutathione (GSH), superoxide dismutase (SOD), and peroxidase (POD) content. Additionally, metabolite profiling was conducted using gas chromatography combined with time-of-flight mass spectrometry (GC/TOF-MS). Phenotypically, the RI alfalfa exhibited a greater resistance to alkali stress than the NI plants examined. Physiological analysis and metabolic profiling revealed that RI plants accumulated more antioxidants (SOD, POD, GSH), osmolytes (sugar, glycols, proline), organic acids (succinic acid, fumaric acid, and alpha-ketoglutaric acid), and metabolites that are involved in nitrogen fixation. Our pairwise metabolomics comparisons revealed that RI alfalfa plants exhibited a distinct metabolic profile associated with alkali putative tolerance relative to NI alfalfa plants. Data provide new information about the relationship between non-nodulized, rhizobium-nodulized alfalfa and alkali resistance.
2018-07-27 | MTBLS481 | MetaboLights
Project description:To understand the role of Medicago truncatula NODULE INCEPTION (MtNIN) in nodule development, we analyzed the transcriptome of roots ectopically overexpressing NIN, nodules of weak mutant allele nin-16, and nodules of dnf1-2 mutant.
2021-11-09 | GSE178119 | GEO
Project description:In order to better understand the commonalities and differences in lateral root and nodule development, we compared their organogenesis and correlated this with changes in gene expression. To initiate lateral roots in Medicago truncatula we turned 2-day-old seedlings 135°, before returning them to their original axis of growth, while for nodule initiation we applied droplets of Sinorhizobium meliloti on the susceptibility zone of the root.
2019-09-20 | GSE133612 | GEO
Project description:Rhizobia are soil bacteria that can enter into complex symbiotic relationships with legumes, where rhizobia induce the formation of nodules on the plant root. Inside nodules, rhizobia differentiate into nitrogen-fixing bacteroids that reduce atmospheric nitrogen into ammonia, secreting it to the plant host in exchange for carbon. During the transition from free-living bacteria to bacteroids, rhizobial metabolism undergoes major changes. To investigate the metabolism of bacteroids and contrast it with the free-living state, we quantified the proteome of unlabelled bacteroids relative to 15N-labelled free-living rhizobia. The data were used to build a core metabolic model of pea bacteroids for the strain Rhizobium leguminosarum bv. viciae 3841.
2021-09-09 | PXD019467 | Pride
Project description:Symbiotic nitroegn fixation in functional (Fix+) and non-functional (Fix-) nodules of Vicia faba infected with Rhizobium leguminosarum was investigated using label-free shotgun tandem MS. Proteins involved in symbiotic nitrogen fixation and maintenance of the symbiosis were identified.
2018-05-30 | PXD008548 | Pride
Project description:Legumes perform symbiotic nitrogen fixation through rhizobial bacteroids housed in specialised root nodules. The biochemical process is energy‐intensive and consumes a huge carbon source to generate sufficient reducing power. To maintain the symbiosis, malate is supplied by legume nodules to bacteroids as their major carbon and energy source in return for ammonium ions and nitrogenous compounds. To sustain the carbon supply to bacteroids, nodule cells undergo drastic reorganisation of carbon metabolism. Here, a comprehensive quantitative comparison of the mitochondrial proteomes between root nodules and uninoculated roots was performed using data‐independent acquisition proteomics, revealing the modulations in nodule mitochondrial proteins and pathways in response to carbon reallocation. Corroborated our findings with that from the literature, we believe nodules preferably allocate cytosolic phosphoenolpyruvates towards malate synthesis in lieu of pyruvate synthesis, and nodule mitochondria prefer malate over pyruvate as the primary source of NADH for ATP production. Moreover, the differential regulation of respiratory chain‐associated proteins suggests that nodule mitochondria could enhance the efficiencies of complexes I and IV for ATP synthesis. This study highlighted a quantitative proteomic view of the mitochondrial adaptation in soybean nodules.
2024-07-16 | PXD050301 | Pride
Project description:The secretion of metabolites by plant roots is a key determinant of microbial growth and colonisation. We have used Pisum sativum and its natural symbiont Rhizobium leguminosarum (it can form N2 fixing nodules on pea roots) to study the natural metabolites secreted by roots. To do this root secretion was harvested from pea plants grown under sterile conditions. This root exudate was then concentrated and used as a sole carbon and nitrogen source for growth of the bacteria in the laboratory. These bacteria were harvested in mid-exponential growth and RNA extracted for microarray analysis. As control cultures the bacteria were grown on 30 mM pyruvate as a carbon source and 10 mM ammonium chloride as a nitrogen source and RNA extracted. Two colour microarrays were performed using root exudate cultures versus pyruvate ammonia grown cultures. This was done in biological triplicate.
2016-05-25 | E-MTAB-4790 | biostudies-arrayexpress
Project description:Biological nitrogen fixation (BNF) is a primary input of nitrogen to natural and agricultural systems globally. BNF is a temperature-dependant enzymatic process and can be conducted by microbes (including Rhizobia) hosted symbiotically in root nodules of some plants. Heat shock proteins (Hsps) have been implicated in the process of acquiring thermotolerance or acclimating to elevated temperature, as they play a vital role in maintaining cell integrity and homeostasis during heat stress. Although the BNF response to temperature may crucially impact future ecosystem productivity in the face of global climate change, little is known about Hsp expression in nodules of N-fixing non-agricultural species, such as tropical N-fixing trees in the Fabaceae family. This project aimed to characterize small (15-20kDa) Hsp (sHsp) expression in nodule tissue to examine the biochemical mechanisms of heat response in these tissues. To first identify Hsps in nodule tissues, Vachellia farnesiana and Acacia confusa nodules were excised, heat shock was induced, and protein content was isolated via chemical treatment before separation of protein species and analysis with SDS-PAGE. Two polyacrylamide gels yielded bands in the 15-20 kDa region that displayed differential Coomassie staining, which were sent for further characterization by HPLC-MS analysis for protein sequencing. Ten rhizobial sHsps were detected in these samples in addition to seven Acacia sHsps when compared independently to reference rhizobial and plant proteome databases. In an attempt quantify relative expression of Hsps in nodule and root tissue, we performed western blot experiments using Anti-Hsp20 antibodies raised against human and mouse Hsp proteins, with anti-beta actin loading control. While nonuniform beta-actin expression across tissue types (A. confusa nodules versus root control) prevented quantitative analysis, the experiments validated that Hsp20s are expressed in Acacia nodules as well as in root tissue. These experiments could provide a foundation for future studies that aim to determine variation in responses to key stressors predicted to increase with global climate change and help determine the implications of warming across the tropics and beyond.
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Project description:Various species of rhizobium establish compatible symbiotic relationships with soybean (Glycine max) leading to the formation of nitrogen-fixing nodules in roots. The formation of functional nodules is mediated through complex developmental and transcriptional reprogramming that involves the activity of thousands of plant genes. However, host transcriptome responses that determine the outcome of the symbiotic interactions leading to the formation of functional or non-functional nodules remain unexplored. In this study, we investigated differential compatibilities between rhizobium strains (Bradyrhizobium diazoefficiens USDA 110Bradyrhizobium sp. strain LVM 105) and cultivated and wild soybeans. The nodulation assays revealed that both USDA 110 and LVM 105 strains effectively nodulate G. soja but only USDA 110 can form symbiotic relationships with Williams 82. RNA-seq data revealed that USDA 110 and LVM 105 induce distinct transcriptome programming in functional mature nodules formed on G. soja roots where genes involved in nucleosome assembly, DNA replication, regulation of cell cycle, and defense responses play key roles. Transcriptome comparison also suggested that activation of genes associated with cell wall biogenesis and organization and defense responses together with downregulation of genes involved in the biosynthesis of isoprenoids and antioxidant stress are associated with the formation of non-functional nodules on Williams 82 roots. Moreover, our analysis implies that increased activity of genes involved in oxygen binding, amino acid transport, and nitrate transport differentiates between fully-developed nodules in cultivated versus wild soybeans.
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