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Bradyrhizobium diazoefficiens

ABSTRACT: Genomic and epigenetic comparison of Bradyrhizobium diazoefficiens culture and bacteroids

PROVIDER: PRJNA291146 | ENA |

REPOSITORIES: ENA

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			Action	DRS
	SRR2132071_subreads.fastq.gz	Fastqsanger.gz
	SRR2132511_subreads.fastq.gz	Fastqsanger.gz
	SRR2131772_subreads.fastq.gz	Fastqsanger.gz
	SRR2132512_subreads.fastq.gz	Fastqsanger.gz
	SRR2132532_subreads.fastq.gz	Fastqsanger.gz

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Metabolomic profiling of Bradyrhizobium diazoefficiens-induced root nodules reveals both host plant-specific and developmental signatures

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

Bradyrhizobium diazoefficiens

Project description:Bradyrhizobium diazoefficiens project

| PRJDB9719 | ENA

Bradyrhizobium diazoefficiens

Project description:Bradyrhizobium diazoefficiens overview

| PRJNA211929 | ENA

Bradyrhizobium diazoefficiens USDA110 nodulation of Aeschynomene afraspera is associated with atypical terminal bacteroid differentiation and suboptimal symbiotic efficiency

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

Proteomic Characterization of Bradyrhizobium diazoefficiens bacteroids during soybean root nodules senescence

Project description:The form and physiology of Bradyrhizobium diazoefficiens after the decline of symbiotic nitrogen fixation has been characterized. Proteomic analyses showed that the post-symbiotic B. diazoefficiens undergo metabolic remodeling as well defined groups of proteins declined, increased or remained unchanged from 56 to 119 days after planting suggesting a transition to a hemibiotrophic-like lifestyle. Enzymatic analysis showed distinct patterns in both the cytoplasm and the periplasm. Similar to the bacteroid, the post-symbiotic bacteria rely on a non-citric acid cycle supply of succinate and although viable, they did not demonstrate the ability to grow within the senescent nodule.

2019-11-12 | PXD011604 | Pride

Bradyrhizobium diazoefficiens

Project description:Bradyrhizobium diazoefficiens Genome sequencing and assembly

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Bradyrhizobium diazoefficiens

Project description:Bradyrhizobium diazoefficiens Transcriptome or Gene expression

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Pleiotropic effects of PhaR regulator in Bradyrhizobium diazoefficiens microaerobic metabolism

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

Bradyrhizobium diazoefficiens USDA 110

Project description:Bradyrhizobium diazoefficiens USDA 110 Epigenomics

| PRJNA243968 | ENA

Bradyrhizobium diazoefficiens USDA 110

Project description:Bradyrhizobium diazoefficiens USDA 110 Epigenomics

| PRJNA242419 | ENA