| As a classical model system for symbiotic nitrogen fixation,rhizobium-legume systems have been studied elaborately for decades.Detailed panorama about the molecular mechanism of the communication and coordination between rhizobia and host plants is becoming clearer.Bradyrhizobium diazoefficiens USDA110 is the type species of Bradyrhizobium.After its whole genome sequencing completed in 2002,the corresponding high throughput transcriptome,proteome and metabolome datasets were also established in recent years.Documentation of its interactome is greatly needed.Based on an in silico framework,we reconstructed the genome-scale protein-protein interaction network(PPI network)of B.diazoefficiens USDA110,integrated it with transcriptome and proteome data and systematically studied the complex protein-protein interactions related to the symbiosis system.In this study,the protein-protein interactions of B.diazoefficien USDA110 were inferred by using “Interolog” and domain-based methods and reconstructed into a PPI network.Reliability of the reconstructed PPI network was assessed from four different perspectives: local structural features,subcellular localization,functional similarities and transcriptional correlations of genes.Based on the comparison of PPI network between B.diazoefficiens USDA110 and other rhizobia,we identified 36 conserved functional PPI modules and inferred that the slow growth of B.diazoefficiens USDA110 may owe to the requirement of more protein modifications.Integrated with transcriptome and proteome data,PPI networks representing free-living cell(34541 PPIs,3650 proteins)and symbiotic nitrogen-fixing bacteroid(10473PPIs,1777 proteins)were obtained.Based on the symbiotic nitrogen-fixing PPI network,a core-sub-PPI-network for symbiotic nitrogen fixation was determined(441PPIs,195 proteins).We identified 9 novel functional modules and 11 key protein hubs playing key roles for symbiosis and annotated them.We inferred that NwsA may perform important coordination function in the cross talk between the FixLJ-FixK2-FixK1 cascade and RegSR-NifA cascade pathways related to N2 fixation.The reconstructed genome-scale PPI network of B.diazoefficiens USDA110 may serve as a valuable reference for studying the mechanism underlying the symbiotic nitrogen-fixing system of rhizobia and legumes. |
