title: An integrated proteomics and transcriptomics reference data set provides new insights into the Bradyrhizobium japonicum bacteroid metabolism in soybean root nodules.
abstract: 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 proteome. Integration of transcriptomics data generated under the same conditions (2780 expressed genes) allowed us to compile a comprehensive expression profile of B. japonicum during soybean symbiosis, which comprises 3587 genes/proteins (43% of the predicted B. japonicum genes/proteins). Analysis of this data set revealed both the biases and the complementarity of these global profiling technologies. A functional classification and pathway analysis showed that most of the proteins involved in carbon and nitrogen metabolism are expressed, including a complete set of tricarboxylic acid cycle enzymes, several gluconeogenesis and pentose phosphate pathway enzymes, as well as several proteins that were previously not considered to be present during symbiosis. Congruent results were obtained for B. japonicum bacteroids harvested from soybeans grown under field conditions.
authors.affiliation: ETH, Institute of Microbiology, Zürich, Switzerland.
authors.forename: Nathanaël
authors.initials: N
authors.lastname: Delmotte
authors.forename: Christian H
authors.initials: CH
authors.lastname: Ahrens
authors.forename: Claudia
authors.initials: C
authors.lastname: Knief
authors.forename: Ermir
authors.initials: E
authors.lastname: Qeli
authors.forename: Marion
authors.initials: M
authors.lastname: Koch
authors.forename: Hans-Martin
authors.initials: HM
authors.lastname: Fischer
authors.forename: Julia A
authors.initials: JA
authors.lastname: Vorholt
authors.forename: Hauke
authors.initials: H
authors.lastname: Hennecke
authors.forename: Gabriella
authors.initials: G
authors.lastname: Pessi
mesh_terms: D001426:Bacterial Proteins / Q000378:metabolism; D020369:Bradyrhizobium / Q000235:genetics / Q000378:metabolism*; D002244:Carbon / Q000378:metabolism; D002853:Chromatography, Liquid; D030562:Databases, Protein; D020869:Gene Expression Profiling / Q000379:methods*; D007526:Isoelectric Point; D053858:Metabolic Networks and Pathways; D008970:Molecular Weight; D009584:Nitrogen / Q000378:metabolism; D009586:Nitrogen Fixation; D009696:Nucleic Acids / Q000378:metabolism; D040901:Proteomics / Q000379:methods*; D053204:Root Nodules, Plant / Q000378:metabolism; D013025:Glycine max / Q000382:microbiology*; D013559:Symbiosis; D053719:Tandem Mass Spectrometry
chemical_list: D001426:Bacterial Proteins; D009696:Nucleic Acids; D002244:Carbon; D009584:Nitrogen