Bradyrhizobium japonicum_Bacteroids Time Course
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ABSTRACT:
ORGANISM(S): Bradyrhizobium diazoefficiens USDA 110 Bradyrhizobium japonicum
PROVIDER: GSE60465 | GEO | 2014/11/01
SECONDARY ACCESSION(S): PRJNA258360
REPOSITORIES: GEO
Similar Datasets
Project description:A time-course transcriptomic analysis of bacteroids isolated from soybean plants inoculated with B. japonicum USDA 110, relative to cells cultured in HM-arabinose medium was performed to characterize senescence genes. Four independent biological materials for bacteroids and free-living cells at 6 time points. Seven or eight arrays including dye swap are presented at each time point.
2014-11-01 | E-GEOD-60465 | biostudies-arrayexpress
Project description:A transcriptomic analysis of bacteroids isolated from soybean plants inoculated with B. japonicum USDA 110, relative to cells cultured in HM-arabinose medium was performed and the results combined with two other transcriptomic analyses to form a reiterated pool of transcripts that define genes essential for symbiotic nitrogen fixation.
2014-11-01 | GSE60279 | GEO
Project description:A transcriptomic analysis of bacteroids isolated from soybean plants inoculated with B. japonicum USDA 110, relative to cells cultured in HM-arabinose medium was performed and the results combined with two other transcriptomic analyses to form a reiterated pool of transcripts that define genes essential for symbiotic nitrogen fixation. Four independent biological replicates for bacteroids and free-living cells. Total of 8 arrays including dye swap.
2014-11-01 | E-GEOD-60279 | biostudies-arrayexpress
Project description:Background: During the symbiosis with legumes, Bradyrhizobium japonicum cells infect roots where they induce the formation of root nodules and differentiate into intracellular nitrogen-fixing bacteroids. We used differential RNA-seq (dRNA-seq) for the genome-wide detection of transcriptional start sites (TSSs) in B. japonicum USDA 110 cells grown free-living or as bacteroids in soybean root nodules. Results: A newly developed TSS recognition procedure based on machine learning allowed us to map 15,923 TSSs: 14,360 in free-living bacteria, 4,329 in bacteroids and 2,766 in both living conditions. Using a proteogenomics approach, we provide evidence for the translation of 107 new transcripts including 14 with TSSs in annotated genes. In addition, we provide evidence for 178 shorter or longer proteins, 109 of them with TSS support. Based on our TSS map and a new de novo promoter prediction algorithm, we identified promoter motifs mainly used in nodules (similar to RpoN-dependent promoters) or under both conditions (similar to RpoD-dependent promoters). The data is made available in a generic feature format (GFF) file along with an updated and extended genome annotation comprising promoters, TSSs and terminators. The value of such a TSS and promoter map beyond the identification of novel transcripts and ORFs is illustrated by the experimental analysis of an antisense RNA, which is a by-product of transcriptional interference in a gene encoding a cytochrome P450 highly expressed in nodules. Conclusions: The genome-wide TSS and promoter map along with the extended genome annotation represents a very useful resource for detailed analyses of gene regulation and further systems biology studies on B. japonicum in symbiosis with soybean.
2016-04-18 | GSE69059 | GEO
Project description:Soybean root hair transcriptional response to their inoculation by the symbiotic bacteria B. japonicum involved in soybean nodulation. We used the first generation of an Affymetrix microarray to quantify the abundance of the transcripts from soybean root hair cells inoculated and mock-inoculated by B. japonicum. This experiment was performed on a time-course from 6 to 48 hours after inoculation.
2010-09-16 | GSE24145 | GEO
Project description:Expression data from B. japonicum soybean root nodules including a nodulation time-course experiment with soybean nodules harvested at 10, 13, 21 and 31 dpi and transcriptome of bacteroids formed by a mutant defective in the RNA polymerase transcription factor sigma 54. Two reference data sets were established using B. japonicum cells grown in PSY medium under either aerobic or micro-aerobic conditions. Keywords: genetic modification, time course, growth conditions
2007-07-14 | GSE8478 | GEO
Project description:Soybean root hair transcriptional response to their inoculation by the symbiotic bacteria B. japonicum involved in soybean nodulation. We used the first generation of an Affymetrix microarray to quantify the abundance of the transcripts from soybean root hair cells inoculated and mock-inoculated by B. japonicum. This experiment was performed on a time-course from 6 to 48 hours after inoculation. Soybean seeds were sowed on sterile agar medium and grown for 3 days in a growth chamber before being treated with H2O (mock-inoculated) or B. japonicum (inoculated). Soybean root hair cells were isolated at different time points (6hr, 12hr, 18hr, 24hr, 36hr, 48hr) after treatment. For each time point and condition, 3 or 4 independent biological replicates were produced.
2010-09-16 | E-GEOD-24145 | 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. 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:B. japonicum cells were grown either in minimal medium (BVM) with L-arabinose as carbon and energy source or in complete medium (PSY) containing L-arabinose. Proteins extracted from three replicates of B. japonicum cells grown in complex and minimal medium with L-arabinose until mid-exponential phase were separated on a Tris-HCl polyacrylamide gel. After reduction and carbamidomethylation, the proteins were digested with trypsin (Promega, Madison, WI, USA), and the resulting peptides were separated by RP-HPLC and analyzed by a hybrid LTQ-Orbitrap XL mass spectrometer (Thermo Fisher Scientific, Waltham, MA, USA) interfaced with a nanoelectrospray source. Mass spectra were further processed with an in-house processing pipeline. A total of 3,390 and 3,149 proteins were identified in complex and minimal medium respectively. We identified highly expressed products of candidate genes involved in the degradation of arabinose and suggest that glycolaldehyde is oxidized to glyoxylate and then reduced to glycerate through a glyoxylate carboligase and a tartronate semialdehyde reductase for assimilation and/or converted to oxalate and then oxidized to formate and CO2 through a formyl-CoA transferase (Frc) and an oxalyl-CoA decarboxylase (Oxc) for energy generation. Fragment ion mass spectra were extracted from Thermo RAW files using msconvert (ProteoWizard, version 3.0.3831), merged in one MGF file per gel and searched against a composite B. japonicum USDA 110 protein database (RefSeq NC_004463.1, July 22, 2013) containing 256 common contaminants (e.g. human keratin, trypsin) with the search engine MS-GF+ (MS-GFDB v7747) for a match to fully-tryptic and semi-tryptic peptides with up to two missed cleavage sites with a mass tolerance of 25ppm and with oxidation (M), deamidation (NQ), methylation (DE) as variable modifications and carbamidomethylation (C) as fixed modification. Using the decoy option of MS-GF+, we filtered the list of peptide spectrum matches (PSMs) to an estimated overall FDR of 0.2%, classified the PSMs with PeptideClassifier, and only further considered peptides (tryptic or semi-tryptic) that unambiguously imply one bacterial protein sequence. The FDR at the peptide level amounted to about 1.5%, that at the protein level to about 2.5% when requiring two peptides or three spectra for a protein identification.
2014-01-30 | PXD000487 | Pride
Project description:part of GSE8478: Genome-wide transcript analysis of Bradyrhizobium japonicum bacteroids in soybean root nodules This SuperSeries is composed of the SubSeries listed below.
2007-11-15 | GSE9100 | GEO