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Identification of genes regulated by the antitermination factor NasT during denitrification in Bradyrhizobium diazoefficiens.

ABSTRACT: Identification of genes regulated by the antitermination factor NasT during denitrification in Bradyrhizobium diazoefficiens.

PROVIDER: PRJNA535436 | ENA |

REPOSITORIES: ENA

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			Action	DRS
	SRR8955130_1.fastq.gz	Fastqsanger.gz
	SRR8955130_2.fastq.gz	Fastqsanger.gz
	SRR8955140_1.fastq.gz	Fastqsanger.gz
	SRR8955140_2.fastq.gz	Fastqsanger.gz
	SRR8955150_1.fastq.gz	Fastqsanger.gz

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Similar Datasets

Identification of genes regulated by the antitermination factor NasT during denitrification in Bradyrhizobium diazoefficiens.

Project description:Purpose: Identification of genes regulated by NasT during denitrifying growth in B. diazoefficiens. Methods: Two biological replications were processed for each strain (wild-type USDA 110 and ΔnasT mutant). Sequencing was performed in an Illumina HiSeq 2000 Sequencing System in paired-end mode running 100x2 cycles (performed by Hokkaido System Science Co., Ltd.). Mapping of reads to the reference genome, read counting, normalization to RPKM (reads per kilobase per million mapped reads), and calculations of expression values were performed with default values with the CLC Genomic Workbench software 9.5.3. From the total reads that were generated, ~85% were trimmed, and from those, ~42% could be mapped onto the B. diazoefficiens genome. Genes with fewer than 10 reads per 1 million mRNA reads were omitted from the following analysis. A gene with a fold change ≥2 or ≤‒2 and a q value (estimate of false discovery rate) ≤0.05 was considered up- or down- regulated, respectively. The results were validated by qRT–PCR. Conclusion: A total of 77 genes were differentially expressed in the ∆nasT mutant compared to those of the wild-type strain, with 38 genes decreased and 37 genes increased in the ∆nasT mutant. Most of these genes were related to nitrogen metabolism.

2019-04-26 | GSE130301 | GEO

Identification of Genes Regulated by the Antitermination Factor NasT during Denitrification in Bradyrhizobium diazoefficiens.

Project description:The soybean symbiont Bradyrhizobium diazoefficiens grows anaerobically in the presence of nitrate using the denitrification pathway, which involves the nap, nir, nor, and nos genes. We previously showed that NasT acts as a transcription antitermination regulator for nap and nos gene expression. In the present study, we investigated the targets of NasT in B. diazoefficiens during denitrifying growth by performing transcription profiling with RNA-seq and quantitative reverse-transcription PCR. Most of the genes with altered expression in the absence of NasT were related to nitrogen metabolism, specifically several systems for branched-chain amino acid transport. The present results suggest that the reduced expression of genes involved in nitrogen acquisition leads to the induction of alternative sets of genes with similar functions. The ?nasT mutant of B. diazoefficiens grew better than the wild type under denitrifying conditions. However, this enhanced growth was completely abolished by an additional loss of the narK or bjgb genes, which encode cytoplasmic systems for nitrite and nitric oxide detoxification, respectively. Since the expression of narK and bjgb was increased in the ?nasT mutant, the growth of the ?nasT mutant may be promoted by increased detoxification activity.

| S-EPMC6759348 | biostudies-literature

Expanding the regulon of the Bradyrhizobium diazoefficiens NnrR transcription factor: New insights into denitrification pathway

Project description:Genome-wide transcription profiling of B. diazoefficiens (formerly B. japonicum) wild type and nnrR mutant strain which were grown in free-living anoxic denitrifying conditions (using nitrate as final electron aceptor). This study includes also the expression data of the wild type strain grown oxically (samples GSM210269 to GSM210283 in GEO record number GSE8478). Keywords: CRP/FNR proteins, in vitro transcription, microoxia, nitrogen oxides, Rhizobia, transcriptomics

2019-08-22 | GSE130684 | GEO

Bradyrhizobium diazoefficiens

Project description:Bradyrhizobium diazoefficiens project

| PRJDB9719 | ENA

Bradyrhizobium diazoefficiens

Project description:Bradyrhizobium diazoefficiens overview

| PRJNA211929 | ENA

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

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 Transcriptome or Gene expression

| PRJNA945098 | ENA

Bradyrhizobium diazoefficiens

Project description:Bradyrhizobium diazoefficiens Genome sequencing and assembly

| PRJNA376228 | ENA

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

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