Glycine max
Ontology highlight
ABSTRACT:
PROVIDER: PRJNA938595 | ENA |
REPOSITORIES: ENA
Dataset's files
| Action | DRS | |||
|---|---|---|---|---|
| SRR23873981_1.fastq.gz | Fastqsanger.gz | |||
| SRR23873981_2.fastq.gz | Fastqsanger.gz | |||
| SRR23873982_1.fastq.gz | Fastqsanger.gz | |||
| SRR23873982_2.fastq.gz | Fastqsanger.gz | |||
| SRR23873983_1.fastq.gz | Fastqsanger.gz |
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Project description:To dissect differences in gene expression profile of soybean roots and root nodules, we have employed microarray analysis. Seeds of soybean (Glycine max L. cv. Nourin No. 2) were inoculated with rhizobia (Bradyrhizobium diazoefficiens USDA110) and were hydroponically cultivated under controlled conditions with nitrogen free culture solution (Saito et al. 2014). At 19 days after planting, each plant were treated with or without 5 mM nitrate for 24 hours. Roots and nodules from three plants were pooled with three biological replications, and total RNA was extracted.
2018-10-01 | GSE104582 | GEO
Project description:Metabolomics and transcriptomics of Bradyrhizobium diazoefficiens-induced root nodules Bradyrhizobium diazoefficiens is a nitrogen-fixing endosymbiont, which can grow inside root-nodule cells of the agriculturally important soybean and other host plants. Our previous studies described B. diazoefficiens host-specific global expression changes occurring during legume infection at the transcript and protein level. In order to further characterize nodule metabolism, we here determine by flow injection -time of flight mass spectrometry analysis the metabolome of i) nodules and roots from four different B. diazoefficiens host plants, ii) soybean nodules harvested at different time points during nodule development, and iii) soybean nodules infected by two strains mutated in key genes for nitrogen fixation, respectively. Ribose (soybean), tartaric acid (mungbean), hydroxybutanoyloxybutanoate (siratro) and catechol (cowpea) were among the metabolites found to be specifically elevated in one of the respective host plants. While the level of C4-dicarboxylic acids decreased during soybean nodule development, we observed an accumulation of trehalose-phosphate at 21 days post infection (dpi). Moreover, nodules from non-nitrogen-fixing bacteroids (nifA and nifH mutants) showed specific metabolic alterations; these were also supported by transcriptomics data that was generated for the two mutant strains and were helpful to separate for some examples the respective bacterial and plant contributions to the metabolic profile. The alterations included signs of nitrogen limitation in both mutants, and an increased level of a phytoalexin in nodules induced by the nifA mutant, suggesting that the tissue of these nodules exhibits defense and stress reactions.
2016-11-28 | GSE79811 | GEO
Project description:The soybean–Bradyrhizobium symbiosis enables symbiotic nitrogen fixation (SNF) within root nodules, reducing reliance on synthetic N fertilizers. However, nitrogen fixation is transient, peaking several weeks after Bradyrhizobium colonization and declining as nodules senesce in coordination with host development. To investigate the regulatory mechanisms governing SNF and senescence, we conducted a temporal transcriptomic analysis of soybean nodules colonized with Bradyrhizobium diazoefficiens USDA110. Weekly nodule samples (2 to 10 weeks postinoculation, wpi) were analyzed using RNA and small RNA sequencing, and acetylene reduction assays assessed nitrogenase activity from 4 to 7 wpi. We identified three major nodule developmental phases: early development (2 to 3 wpi), nitrogen fixation (3 to 8 wpi), and senescence (8 to 10 wpi). Soybean showed extensive transcriptional reprogramming during senescence, whereas Bradyrhizobium underwent major transcriptional shifts early in development before stabilizing during nitrogen fixation. We identified seven soybean genes and several microRNAs as candidate biomarkers of nitrogen fixation, including lipoxygenases (Lox), suggesting roles for oxylipin metabolism. Soy hemoglobin-2 (Hb2), previously classified as nonsymbiotic, was upregulated during senescence, implicating oxidative stress responses within aging nodules. Upregulation of the Bradyrhizobium paa operon and rpoH during senescence suggesting metabolic adaptation for survival beyond symbiosis. Additionally, Bradyrhizobium nif gene expression showed stage-specific regulation, with nifK peaking at 2 wpi, nifD and nifA at 2 and 10 wpi, and nifH, nifW, and nifS at 10 wpi. These findings provide insights into SNF regulation and nodule aging, revealing temporal gene expression patterns that could inform breeding or genetic engineering strategies to enhance nitrogen fixation in soybeans and other legume crops.
2025-12-29 | GSE289665 | GEO
Project description:Legume plants can form root organs called nodules where they house intracellular symbiotic rhizobium bacteria. Within nodule cells, rhizobia differentiate into bacteroids, which fix nitrogen for the benefit of the plant. Depending on the combination of host plants and rhizobial strains, the output of rhizobium-legume interactions is varying from non-fixing associations to symbioses that are highly beneficial for the plant. Bradyrhizobium diazoefficiens USDA110 was isolated as a soybean symbiont but it can also establish a functional symbiotic interaction with Aeschynomene afraspera. In contrast to soybean, A. afraspera triggers terminal bacteroid differentiation, a process involving bacterial cell elongation, polyploidy and membrane permeability leading to loss of bacterial viability while plants increase their symbiotic benefit. A combination of plant metabolomics, bacterial proteomics and transcriptomics along with cytological analyses was used to study the physiology of USDA110 bacteroids in these two host plants. We show that USDA110 establish a poorly efficient symbiosis with A. afraspera, despite the full activation of the bacterial symbiotic program. We found molecular signatures of high level of stress in A. afraspera bacteroids whereas those of terminal bacteroid differentiation were only partially activated. Finally, we show that in A. afraspera, USDA110 bacteroids undergo an atypical terminal differentiation hallmarked by the disconnection of the canonical features of this process. This study pinpoints how a rhizobium strain can adapt its physiology to a new host and cope with terminal differentiation when it did not co-evolve with such a host.
2020-12-11 | GSE163004 | GEO
Project description:The nuclei of Glycine max root seedlings (6 days-old) and nodules (28 days-old) were isolated and the library consstruction was performed applying 10x Genomics tecnology.
2024-07-08 | GSE226149 | GEO
Project description:Bradyrhizobium diazoefficiens can live inside soybean root nodules and in free-living conditions. In both states, when oxygen levels decrease, cells adjust their protein pools by gene transcription modulation. PhaR encodes a transcription factor annotated as PHA (polyhydroxyalkanoate) accumulation regulator. We found that PhaR not only controls the PHA cycle but also acts as a global regulator of excess carbon allocation by controlling the expression of fixK2 and nifA genes, both encoding key transcription factors for microoxic and symbiotic metabolism in B. diazoefficiens. The function of PhaR was expanded by a multi-pronged approach that includes analysis of the effects of phaR mutation at transcriptional and protein levels of putative PhaR targets and direct control mediated by PhaR determined by EMSA assays. We also were able to identify PhaR, phasins and other proteins associated with PHA granules which confirmed a global function of PhaR in microoxia.
2024-05-22 | PXD047760 | Pride
Project description:RNA-Seq of Glycine max roots: Transcriptomic profiling of GmMYB62s knockout mutant (myb62-1) vs. wild-type (Williams 82) during early nodulation with Bradyrhizobium japonicum USDA110 (PRJCA042702)
| PRJDB38856 | ENA
Project description:dual Transcriptome of Glycine max and Bradyrhizobium diazoefficiens USDA110
| PRJNA938529 | ENA
Project description:part of GSE8478: Genome-wide transcript analysis of Bradyrhizobium japonicum bacteroids in soybean root nodules This SuperSeries is composed of the SubSeries listed below.
2007-11-15 | GSE9100 | GEO
Project description:The transition metal tungsten (W) finds increasing application in military, aviation and household appliance industry, opening new paths for the heavy metal into the environment. Since tungsten shares certain chemical properties with the essential plant micro nutrient molybdenum, it is proposed to inhibit enzymatic activity of molybdoenzymes by replacing the Mo-ion bound to the co-factor. However, recent studies suggest the inhibition of enzymatic activity might not be the only effect W has on plants and that, much like other heavy metals, tungsten exerts toxicity on its own. Still, our understanding of the mechanisms behind the apparent phytotoxicity remains limited.This study investigates the effects of W on growth, nutrient levels (ionome, ICP-MS), starch levels and nitrogen nutrition (IRMS, enzyme activity assays) as well as root and nodule proteome (LC-MS/MS) of Glycine max cv. Primus. Plants were inoculated with Bradyrhizobium japonicum and grown in a semi hydroponic set up using three different tungsten concentrations (zero, 0.1 mM and 0.5 mM). To identify possible benefits of a functional bacterial symbiosis on W induced stress response, two different environmental growth conditions, one with suppressed N-fixation, supplied with Nitrate (10 mM KNO3) and one solely relying on symbiotic N-fixation (zero KNO3), were applied. Glycine max was able to take up considerable amounts of W (703 ± 136 mg kg-1). However, high W resulted in a strong reduction of shoot biomass of both N regimes and of root biomass (N fed only). Irrespective of N regime, NR activity and total N decreased with increasing W concentrations. Similarly, nitrogenase precursor levels as well as N2-fixation, nodule fixation activity (mg N g-1 nodule dry weight) and nodulation were reduced, indicating that nitrogenase synthesis and activity were negatively affected by W stress. However, along a N fix nodule specific induction of the secondary and phytohormone metabolism, it appears that N2 fixation of remaining nodules was not as severely affected by increasing levels of tungsten than nitrate reduction. Besides N metabolism, plants exhibited an imbalance in nutrient and a failure of carbon metabolic pathways accompanied by an accumulation of starch at high tungsten concentrations, independent of N-regime. Proteomic data demonstrated that the response to high W concentrations is independent of nodule functionality and dominated by several peroxidases and other general stress related proteins. Based on an evaluation of several W responsive proteotypic peptides, we identified a set of protein markers of W stress and possible targets for improved stress tolerance.
2019-04-09 | PXD010877 | Pride