Computationally reconstructed interactome of Bradyrhizobium diazoefficiens USDA110 reveals novel functional modules and protein hubs for symbiotic nitrogen fixation

Symbiotic nitrogen fixation is an important part of the nitrogen biogeochemical cycles and the main nitrogen source of the biosphere. 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. For more systematic insights, there is an increasing demand on new studies integrating multi-omics information. Here we present a comprehensive computational framework, integrating the reconstructed protein interactome of B. diazoefficiens USDA110 with its transcriptome and proteome data, to study the complex protein-protein interaction (PPI) network involved in the symbiosis system. We reconstructed the interactome of B. diazoefficiens USDA110 by computational approaches. Based on the comparison of interactomes between B. diazoefficiens USDA110 and other rhizobia, we inferred that the slow growth of B. diazoefficiens USDA110 may owe to the requirement of more protein modifications and further identified 36 conserved functional PPI modules. Integrated with transcriptome and proteome data, interactomes representing free-living cell and symbiotic nitrogen-fixing (SNF) bacteroid were obtained. Based on the SNF interactome, a core-sub-PPI-network for symbiotic nitrogen fixation was determined and 9 novel functional modules and 11 key protein hubs playing key roles for symbiosis were identified. The reconstructed interactome of B. diazoefficiens USDA110 may serve as a valuable reference for studying the mechanism underlying the SNF system of rhizobia and legumes.