Global protein expression pattern ofBradyrhizobium japonicum bacteroids: A prelude to functional proteomics

Abstract

As a prelude to using functional proteomics towards understanding the process of symbiotic nitrogen fixation between the legume soybean and the soil bacteria Bradyrhizobium japonicum, we examined the total protein expression pattern of the nodule bacteria, often referred to as bacteroids. A partial proteome map was constructed by separating the total bacteroid proteins using high-resolution 2-DE. Of the several hundred protein spots analyzed using PMF, 180 spots were tentatively identified by searching the available database for B. japonicum, (http://www.kazusa.or.jp/index.html). The data showed that the bacteroid expressed a dominant and elaborate protein network for nitrogen and carbon metabolism, which is closely dependent on the plant supplied metabolites, and seems aptly supported by a selective group of bacteroid transporter proteins. However, they seem to lack a defined fatty acid and nucleic acid metabolism. Interestingly, the proteins related to protein synthesis, scaffolding and degradation were among the most predominant spots of the bacteroid proteome. In addition, several proteins, which showed fairly good expression, were identified to be involved with cellular detoxification, stress regulation and signaling communication components. This preliminary proteomic data matches very well with several biochemical and genetic reports, and clearly shows the inter-connection between several metabolic pathways that meet the needs of the bacteroid. It is expected that in the future this will allow us to develop testable hypotheses about the roles of several of these proteins in context to the metabolic pathway connections and metabolite fluxes.

Metabolic Reconstruction and Modeling of Nitrogen Fixation in Rhizobium etli

“…This last point constitutes a valuable scientific objective which requires integration of experimental data to improve and update the metabolic reconstruction. For instance, aspartate aminotransferase in B. japonicus is essential, and its deletion is detrimental to nitrogen fixation [17], while a deletion of glutamine synthetase increases nitrogen fixation [17]. We do not observe this behavior in silico for R. etli.…”

“…FBA predicts the production of amino acids included in the OF (aspartate, alanine, and lysine). Experimental evidence shows the production of these amino acids in B. japonicum bacteroid [17]. Conversely, the experimental data for the B. japonicum bacteroid disagrees with the in silico analysis for R. etli, where asparagine, methionine, leucine, isoleucine, glycine, glutamine, and serine are not predicted by the model to be produced.…”

“…Similarly, recent studies have shown the ability of Rhizobia to produce amino acids in well-defined environments and the effects that these amino acids have on symbiotic nitrogen fixation [16,17,46]. Although the production of the complete spectrum of amino acids has not been well-characterized in R. etli during nitrogen fixation, we have predicted their production with the model, and compared them with the amino acids experimentally observed in B. japonicum bacteroids [17].…”

“…Although the production of the complete spectrum of amino acids has not been well-characterized in R. etli during nitrogen fixation, we have predicted their production with the model, and compared them with the amino acids experimentally observed in B. japonicum bacteroids [17]. FBA predicts the production of amino acids included in the OF (aspartate, alanine, and lysine).…”

“…In this context, we postulate that symbiotic nitrogen fixation is closely related to the efficient supply of alanine and aspartate from the bacteroid to the plant. L-lysine has been reported in Bradyrhizobium japonicum bacteroids, a related organism to R. etli, and this amino acid was also included in the OF [17].…”