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

ABSTRACT: 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

ORGANISM(S): Bradyrhizobium diazoefficiens Bradyrhizobium diazoefficiens USDA 110

PROVIDER: GSE130684 | GEO | 2019/08/22

REPOSITORIES: GEO

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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

Fine-tuning modulation of oxidation-mediated posttranslational control of Bradyrhizobium diazoefficiens FixK2 transcription factor

Project description:Genome-wide transcription profiling of B. diazoefficiens (formerly B. japonicum) wild type and a C183D FixK2 encoding strain which were cultured under microoxic conditions (0.5% O2). For comparison, this work also includes the expression data samples GSM210246 to GSM210268, and samples GSM313727 to GSM313734 in GEO record number GSE12491. Keywords: CRP/FNR proteins, in vitro transcription, microoxia, posttranslational control, protein-DNA interaction, Rhizobia, transcriptomics

2022-05-05 | GSE196031 | 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

Pleiotropic effects of PhaR regulator in Bradyrhizobium diazoefficiens microaerobic metabolism

Project description:Genome-wide transcription profiling of B. diazoefficiens (formerly B. japonicum) and a phaR mutant, both cultured under microoxic conditions (0.5% O2) in Götz minimal medium supplemented with mannitol. Keywords: microoxia, polyhydroxybutyrate, protein-DNA interaction, proteomics, Rhizobia, transcriptomics

2024-02-28 | GSE250298 | GEO

Bradyrhizobium diazoefficiens

Project description:Bradyrhizobium diazoefficiens project

| PRJDB9719 | ENA

Bradyrhizobium diazoefficiens

Project description:Bradyrhizobium diazoefficiens overview

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Autoregulation of fixK2 gene expression in Bradyrhizobium japonicum

Project description:Expression data from B. japonicum bll2758::aphII strain (7414) grown micro-oxically. This study includes also the expression data of a fixK2 and a fixJ mutant grown in free-living micro-oxic condition (samples GSM313721 to GSM313734 in GEO record number GSE12491) and the wild type strain grown micro-oxically (samples GSM210246 to GSM210268 in GEO record number GSE8478).

2010-06-11 | GSE21400 | GEO

Reactive oxygen species-inducible ECF σ factor involved in singlet-oxygen responsiveness of Bradyrhizobium japonicum

Project description:Expression data from B. japonicum strains 110spc4 (wild type), 0202 (Dbll1028), 9688 (Dblr3038-39) grown micro-oxically unstressed or stressed with 2 mM H2O2 for 10 min and strain 9692 (Dblr3039) grown micro-oxically

2012-08-24 | GSE39165 | GEO

Levels of Periplasmic Nitrate Reductase during Denitrification are Lower in Bradyrhizobium japonicum than in Bradyrhizobium diazoefficiens.

Project description:Soybean plants host endosymbiotic dinitrogen (N2)-fixing bacteria from the genus Bradyrhizobium. Under oxygen-limiting conditions, Bradyrhizobium diazoefficiens and Bradyrhizobium japonicum perform denitrification by sequentially reducing nitrate (NO3-) to nitrous oxide (N2O) or N2. The anaerobic reduction of NO3- to N2O was previously shown to be lower in B. japonicum than in B. diazoefficiens due to impaired periplasmic nitrate reductase (Nap) activity in B. japonicum. We herein demonstrated that impaired Nap activity in B. japonicum was due to low Nap protein levels, which may be related to a decline in the production of FixP and FixO proteins by the cbb3-type oxidase.

| S-EPMC7511789 | biostudies-literature

The copper-responsive regulator CsoR is indirectly involved in Bradyrhizobium diazoefficiens denitrification.

Project description:The soybean endosymbiont Bradyrhizobium diazoefficiens harbours the complete denitrification pathway that is catalysed by a periplasmic nitrate reductase (Nap), a copper (Cu)-containing nitrite reductase (NirK), a c-type nitric oxide reductase (cNor), and a nitrous oxide reductase (Nos), encoded by the napEDABC, nirK, norCBQD, and nosRZDFYLX genes, respectively. Induction of denitrification genes requires low oxygen and nitric oxide, both signals integrated into a complex regulatory network comprised by two interconnected cascades, FixLJ-FixK2-NnrR and RegSR-NifA. Copper is a cofactor of NirK and Nos, but it has also a role in denitrification gene expression and protein synthesis. In fact, Cu limitation triggers a substantial down-regulation of nirK, norCBQD, and nosRZDFYLX gene expression under denitrifying conditions. Bradyrhizobium diazoefficiens genome possesses a gene predicted to encode a Cu-responsive repressor of the CsoR family, which is located adjacent to copA, a gene encoding a putative Cu+-ATPase transporter. To investigate the role of CsoR in the control of denitrification gene expression in response to Cu, a csoR deletion mutant was constructed in this work. Mutation of csoR did not affect the capacity of B. diazoefficiens to grow under denitrifying conditions. However, by using qRT-PCR analyses, we showed that nirK and norCBQD expression was much lower in the csoR mutant compared to wild-type levels under Cu-limiting denitrifying conditions. On the contrary, copA expression was significantly increased in the csoR mutant. The results obtained suggest that CsoR acts as a repressor of copA. Under Cu limitation, CsoR has also an indirect role in the expression of nirK and norCBQD genes.

| S-EPMC10457146 | biostudies-literature

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