Bradyrhizobium japonicum
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ABSTRACT:
PROVIDER: PRJNA244265 | ENA |
REPOSITORIES: ENA
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Project description:Analysis of a Bradyrhizobium japonicum pmtA mutant. PmtA catalyzes the first of three consecutive methylation reactions leading to phosphatidylcholine (PC) formation in B. japonicum. Disruption of the pmtA gene results in a significantly reduced PC content causing a defect in symbiosis with the soybean host. This study provides the first insight into global transcriptomic changes of a bacterial phosphatidylcholine biosynthesis mutant. Cells of the pmtA mutant and the wild type were grown to mid-exponential phase in full medium (PSY) under aerobic culture conditions. Keywords: genetic modification
2008-04-17 | GSE11187 | GEO
Project description:Analysis of a Bradyrhizobium japonicum pmtA mutant. PmtA catalyzes the first of three consecutive methylation reactions leading to phosphatidylcholine (PC) formation in B. japonicum. Disruption of the pmtA gene results in a significantly reduced PC content causing a defect in symbiosis with the soybean host. This study provides the first insight into global transcriptomic changes of a bacterial phosphatidylcholine biosynthesis mutant. Cells of the pmtA mutant and the wild type were grown to mid-exponential phase in full medium (PSY) under aerobic culture conditions. Keywords: genetic modification Comparative analyis of the B. japonicum pmtA mutant and the wild type grown under aerobic culture conditions.
2008-04-17 | E-GEOD-11187 | biostudies-arrayexpress
Project description:The Bradyrhizobium japonicum NtrC regulatory protein influences gene expression in response to changes in intracellular nitrogen status. Under conditions of low nitrogen, phosphorylation of NtrC results in up-regulation of a number of genes involved in nitrogen metabolism and nitrogen acquisition. To better define the exact nature of NtrC’s influence on gene expression, a ntrC mutation was created in B. japonicum and transcriptional profiling was performed by DNA microarray analysis of both the mutant and wild type strains.
2015-06-25 | GSE66091 | GEO
Project description:The Bradyrhizobium japonicum NtrC regulatory protein influences gene expression in response to changes in intracellular nitrogen status. Under conditions of low nitrogen, phosphorylation of NtrC results in up-regulation of a number of genes involved in nitrogen metabolism and nitrogen acquisition. To better define the exact nature of NtrC’s influence on gene expression, a ntrC mutation was created in B. japonicum and transcriptional profiling was performed by DNA microarray analysis of both the mutant and wild type strains.
2012-07-01 | GSE23870 | GEO
Project description:Elevated atmospheric CO2 can influence the structure and function of rhizosphere microorganisms by altering root growth and the quality and quantity of compounds released into the rhizosphere via root exudation. In these studies we investigated the transcriptional responses of Bradyrhizobium japonicum cells growing in the rhizosphere of soybean plants exposed to elevated atmospheric CO2. The results of microarray analyses indicated that atmospheric elevated CO2 concentration indirectly influences on expression of large number of Bradyrhizobium genes through soybean roots. In addition, genes involved in C1 metabolism, denitrification and FixK2-associated genes, including those involved in nitrogen fixation, microanaerobic respiration, respiratory nitrite reductase, and heme biosynthesis, were significantly up-regulated under conditions of elevated CO2 in the rhizosphere, relative to plants and bacteria grown under ambient CO2 growth conditions. The expression profile of genes involved in lipochitinoligosaccharide Nod factor biosynthesis and negative transcriptional regulators of nodulation genes, nolA and nodD2, were also influenced by plant growth under conditions of elevated CO2. Taken together, results of these studies indicate that growth of soybeans under conditions of elevated atmospheric CO2 influences gene expressions in B. japonicum in the soybean rhizosphere, resulting in changes to carbon/nitrogen metabolism, respiration, and nodulation efficiency.
2010-07-29 | GSE23296 | GEO
Project description:Bradyrhizobium japonicum RegSR regulatory proteins belong to the family of two-component regulatory systems, and orthologs are present in many Proteobacteria where they globally control gene expression mostly in a redox-responsive manner. In this work, we have performed a transcriptional profiling of wild-type and regR mutant cells grown under anoxic denitrifying conditions. The comparative analyses of wild-type and regR strains revealed that almost 620 genes induced in the wild type under denitrifying conditions were regulated (directly or indirectly) by RegR, pointing out the important role of this protein as a global regulator of denitrification. Genes controlled by RegR included nor and nos structural genes encoding nitric oxide and nitrous oxide reductase, respectively, genes encoding electron transport proteins such as cycA (blr7544), or cy2 (bll2388), genes involved in nitric oxide detoxification (blr2806-09), copper homeostasis (copCAB), as well as two regulatory genes (bll3466, bll4130). Purified RegR interacted with the promoters of norC (blr3214), nosR (blr0314), a fixK-like gene (bll3466), and bll4130 which encodes a LysR-type regulator. By using fluorescently labeled oligonucleotide extension (FLOE), we were able to identify two transcriptional start sites located at about 35 (P1) and 22 (P2) bp upstream of the putative translational start codon of norC. P1 matched with the previously mapped 5M-bM-^@M-^Yend of norC mRNA which we demonstrate in this work to be under FixK2 control. P2 is a start site modulated by RegR and specific for anoxic conditions. Moreover, qRT-PCR experiments, expression studies with a norC-lacZ fusion, and heme c-staining analyses revealed that anoxia and nitrate are required for RegR-dependent induction of nor genes, and that this control is independent of the sensor protein RegS. A total of eight Affymetrix GeneChips are included in this study. Per strain (wild-type B. japonicum 110spc4, delta regR mutant 2426) four biological replicates were processed and analyzed. Strains were grown under anoxic conditions in Bergersen minimal medium supplemented with succinate as carbon source and KNO3 as terminal electron acceptor. For comparison, a microarray expression dataset generated with B. japonicum wild-type (Hauser et al., Mol. Genet. Genomics 278:255-271, 2007) and delta regR mutant cells (Lindemann et al., J. Bacteriol. 189:8928-8943, 2007) was used.
2014-09-01 | E-GEOD-56668 | biostudies-arrayexpress
Project description:The purpose of the study is to identify Irr-responsive genes in the bacterium Bradyrhizobium japonicum. Parent strain LO was compared to irr mutant strain LODTM5 by whole genome microarray analysis. Both cell types were grown in iron-limited media. Keywords: Comparison of B. japonicum wild type and mutant cells
2006-03-15 | GSE4155 | GEO
Project description:The Bradyrhizobium japonicum NtrC regulatory protein influences gene expression in response to changes in intracellular nitrogen status. Under conditions of low nitrogen, phosphorylation of NtrC results in up-regulation of a number of genes involved in nitrogen metabolism and nitrogen acquisition. To better define the exact nature of NtrC’s influence on gene expression, a ntrC mutation was created in B. japonicum and transcriptional profiling was performed by DNA microarray analysis of both the mutant and wild type strains. Bradyrhizobium japonicum USDA 110 and a ntrC mutant in the USDA 110 background were cultured in minimal medium supplemented with either 10mM glutamate (low nitrogen) or 10mM ammonium and 10mM glutamate (high nitrogen) as nitrogen sources. Four comparisons were performed: wild type high nitrogen vs. mutant high nitrogen, wild type low nitrogen vs. wild type high nitrogen, wild type low nitrogen vs. mutant low nitrogen, and mutant low nitrogen vs. mutant high nitrogen. For each of the four comparisons, three biological replicates were prepared for each strain and dye swap replications were performed for each hybridization producing a total of six arrays per comparison and 24 arrays in total.
2015-06-25 | E-GEOD-66091 | biostudies-arrayexpress
Project description:Copper-regulated genes of Bradyrhizobium japonicum
| PRJNA174042 | ENA
Project description:Legumes interact with nodulating bacteria that convert atmospheric nitrogen into ammonia for plant use. This nitrogen fixation takes place within root nodules that form after infection of root hairs by compatible rhizobia. Using cDNA microarrays, we monitored gene expression in soybean (Glycine max) inoculated with the nodulating bacterium Bradyrhizobium japonicum 4, 8, and 16 days after inoculation (dai), time points that coincided with nodule development and the onset of nitrogen fixation. This experiment identified several thousand genes that were differentially expressed in response to B. japonicum inoculation. Expression of 27 genes was analyzed by qRT-PCR and their expression patterns mimicked the microarray results confirming integrity of analyses. The microarray results suggest that B. japonicum reduces plant defense responses during nodule development. In addition, the data revealed a high level of regulatory complexity (transcriptional, post-transcriptional, translational, post-translational) that is likely essential for development of the symbiosis and adjustment to an altered nutritional status. Keywords = symbiosis Keywords = nodulation Keywords = rhizobium Keywords = defense Keywords = ANOVA Keywords = plant loop design, 7 samples, 7 comparison, 2 technical repeats including dye swaps, 4 biological repeats
2008-02-04 | E-GEOD-10340 | biostudies-arrayexpress