Abstract
Mesorhizobium huakuii 7653R occurs either in nitrogen-fixing symbiosis with its host plant, Astragalus sinicus, or free-living in the soil. The M. huakuii 7653R genome has recently been sequenced. To better understand the complex biochemical and developmental changes that occur in 7653R during bacteroid development, RNA-Seq and Microarrays were used to investigate the differential transcriptomes of 7653R bacteroids and free-living cells. The two approaches identified several thousand differentially expressed genes. The most prominent up-regulation occurred in the symbiosis plasmids, meanwhile gene expression is concentrated to a set of genes (clusters) in bacteroids to fulfill corresponding functional requirements. The results suggested that the main energy metabolism is active while fatty acid metabolism is inactive in bacteroid and that most of genes relevant to cell cycle are down-regulated accordingly. For a global analysis, we reconstructed a protein-protein interaction (PPI) network for 7653R and integrated gene expression data into the network using Cytoscape. A highly inter-connected subnetwork, with function enrichment for nitrogen fixation, was found, and a set of hubs and previously uncharacterized genes participating in nitrogen fixation were identified. The results described here provide a broader biological landscape and novel insights that elucidate rhizobial bacteroid differentiation, nitrogen fixation and related novel gene functions.
Highlights
Rhizobia are specific soil bacteria, which can establish an intricate symbiotic relationship with Legumes
As bacteroids are enclosed by a peribacteroid membrane of plant origin [34], it is difficult to extract bacteroids RNA from nodules, from the nodules of A. sinicus induced by M. huakuii 7653R because of their smaller size
The RNA sequencing (RNA-Seq) method used in this study examines a larger range of differential gene expression levels
Summary
Rhizobia are specific soil bacteria, which can establish an intricate symbiotic relationship with Legumes This interaction results in the formation of specialized root structures called nodules [1]. The host plant provides rhizobia with dicarboxylic acids as a source of carbon, energy, and reductant [4] and ammonium (via N2 reduction that occurs in these bacteroids) is secreted back to the plant. This biological process serves as a natural form of fertilization and has significant potential for use in sustainable agricultural programs, especially if optimized. Rhizobiumlegume symbiosis has been the subject of much study for decades
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