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Proteins of B. japonicum expressed in siratro nodules

ABSTRACT: Proteins of B. japonicum expressed in soybean nodules

INSTRUMENT(S): LTQ Orbitrap, instrument model

ORGANISM(S): Bradyrhizobium Japonicum Bradyrhizobium Japonicum Usda 110

SUBMITTER: Nathanael Delmotte

PROVIDER: PRD000813 | Pride | 2010-04-29

REPOSITORIES: Pride

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			Action	DRS
	PRIDE_Exp_Complete_Ac_10112.pride.mgf.gz	Mgf
	PRIDE_Exp_Complete_Ac_10112.xml.gz	Xml
	PRIDE_Exp_Complete_Ac_10113.pride.mgf.gz	Mgf
	PRIDE_Exp_Complete_Ac_10113.xml.gz	Xml
	PRIDE_Exp_Complete_Ac_10114.pride.mgf.gz	Mgf

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Publications

An integrated proteomics and transcriptomics reference data set provides new insights into the Bradyrhizobium japonicum bacteroid metabolism in soybean root nodules.

Delmotte Nathanaël N Ahrens Christian H CH Knief Claudia C Qeli Ermir E Koch Marion M Fischer Hans-Martin HM Vorholt Julia A JA Hennecke Hauke H Pessi Gabriella G

Proteomics 20100401 7

Bradyrhizobium japonicum, a gram-negative soil bacterium that establishes an N(2)-fixing symbiosis with its legume host soybean (Glycine max), has been used as a symbiosis model system. Using a sensitive geLC-MS/MS proteomics approach, we report the identification of 2315 B. japonicum strain USDA110 proteins (27.8% of the theoretical proteome) that are expressed 21 days post infection in symbiosis with soybean cultivated in growth chambers, substantially expanding the previously known symbiosis ...[more]

PMID: 20104621

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Proteins of B. japonicum expressed in cowpea nodules

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2010-05-17 | PRD000766 | Pride

Genome-wide transcript analysis of Bradyrhizobium japonicum bacteroids in soybean root nodules

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

Comparison analysis of B. japonicum mutant and wild type grown under different conditions

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

Shotgun proteomics of soybean root nodules infected by Bradyrhizobium japonicum

Project description:Global bottom-up proteomics analysis of proteins purified from soybean root nodules infected with either WT or nifH- mutant Bradyrhizobium japonicum. Nine glycoproteins containing Lewis-a N-glycans, with 3 distinct Lewis-a epitopes (Hex:5 HexNAc:4 dHex:3 Pent:1, Hex:4 HexNAc:4 dHex:2 Pent:1, and Hex:4 HexNAc:3 dHex:2 Pent:1) were observed. Proteins purified from WT and nifH- infected soybean root nodules (five biological replicates each) were reduced using dithiothreitol, alkylated with iodoacetamide and trypsin digested followed by C18 SPE clean-up and LC-MS/MS analysis. Raw data files were processed using FragPipe v17.1, then output files 'combined_modified_peptide.tsv' and 'combined_protein.tsv' were used to identify glycopeptides and for global protein quantitation. These files, along with Excel files containing global quantitation analysis files for soybean nodule (Glycine max) and bacterial (Bradyrhizobium), are available in directory 'Quantification/MSFragger_results'. Glycopeptide data were also processed with PMI Byonic, and Excel file results are available in directory 'Quantification/PMI_Byonic_results'.

2022-01-31 | MSV000088754 | MassIVE

Genome-wide transcription start site mapping of Bradyrhizobium japonicum free-living cells and bacteroids - a rich resource to identify new transcripts, proteins and to study gene regulation

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

Transcription profiling of soybean nodulation by Bradyrhizobium japonicum

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

Comprehensive assessment of the regulons controlled by the FixLJ-FixK2-FixK1 cascade in Bradyrhizobium japonicum

Project description:Genome-wide transcription profiling of B. japonicum fixJ, fixK2, and fixK1 mutant strains which were grown in free-living microoxic condition, and in the case of the fixK1 mutant also in anoxic condition. Transcriptomes of nodules from soybean plants infected with the fixJ or fixK2 mutant strains were investigated, too. This study includes also the expression data of a nifA mutant grown in free-living anoxic condition. Samples from GSM210242 to GSM210286 in GEO record number GSE8478 need to be considered for the analyses. Keywords: gene regulation, genetic modification, growth conditions, symbiosis Comparison analysis of the B. japonicum fixJ, fixK2 and fixK1 mutants and the wild type grown under different oxygen conditions in culture and during symbiosis with soybean.

2010-05-23 | E-GEOD-12491 | biostudies-arrayexpress

Transcription profiling of soybean nodulation by Bradyrhizobium japonicum

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Soybean root hair cell response to Bradyrhizobium japonicum inoculation

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.

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