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

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

PROVIDER: PRJNA540979 | ENA |

REPOSITORIES: ENA

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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

Expanding the Regulon of the Bradyrhizobium diazoefficiens NnrR Transcription Factor: New Insights Into the Denitrification Pathway.

Project description:Denitrification in the soybean endosymbiont Bradyrhizobium diazoefficiens is controlled by a complex regulatory network composed of two hierarchical cascades, FixLJ-FixK2-NnrR and RegSR-NifA. In the former cascade, the CRP/FNR-type transcription factors FixK2 and NnrR exert disparate control on expression of core denitrifying systems encoded by napEDABC, nirK, norCBQD, and nosRZDFYLX genes in response to microoxia and nitrogen oxides, respectively. To identify additional genes controlled by NnrR and involved in the denitrification process in B. diazoefficiens, we compared the transcriptional profile of an nnrR mutant with that of the wild type, both grown under anoxic denitrifying conditions. This approach revealed more than 170 genes were simultaneously induced in the wild type and under the positive control of NnrR. Among them, we found the cycA gene which codes for the c 550 soluble cytochrome (CycA), previously identified as an intermediate electron donor between the bc 1 complex and the denitrifying nitrite reductase NirK. Here, we demonstrated that CycA is also required for nitrous oxide reductase activity. However, mutation in cycA neither affected nosZ gene expression nor NosZ protein steady-state levels. Furthermore, cycA, nnrR and its proximal divergently oriented nnrS gene, are direct targets for FixK2 as determined by in vitro transcription activation assays. The dependence of cycA expression on FixK2 and NnrR in anoxic denitrifying conditions was validated at transcriptional level, determined by quantitative reverse transcription PCR, and at the level of protein by performing heme c-staining of soluble cytochromes. Thus, this study expands the regulon of NnrR and demonstrates the role of CycA in the activity of the nitrous oxide reductase, the key enzyme for nitrous oxide mitigation.

| S-EPMC6710368 | biostudies-literature

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

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

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

| PRJNA535436 | ENA

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

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

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Project description:Bradyrhizobium diazoefficiens Transcriptome or Gene expression

| PRJNA945098 | ENA

Bradyrhizobium diazoefficiens

Project description:Bradyrhizobium diazoefficiens Genome sequencing and assembly

| PRJNA376228 | ENA