Computationally Reconstructed Interactome of Bradyrhizobium diazoefficiens USDA110 Reveals Novel Functional Modules and Protein Hubs for Symbiotic Nitrogen Fixation

• Published in: International journal of molecular sciences 2021-11, Vol.22 (21), p.11907
• Main Authors: Ma, Jun-Xiao, Yang, Yi, Li, Guang, Ma, Bin-Guang
• Format: Article
• Language: English
• Subjects: Bacterial Proteins - genetics; Bacterial Proteins - metabolism; Biogeochemical cycles; Biosphere; Bradyrhizobium - genetics; Bradyrhizobium - growth & development; Bradyrhizobium - metabolism; Computer applications; data integration; Genomes; Glycine max - microbiology; Host plants; Hubs; Legumes; Methods; Molecular modelling; multiomics; network analysis; Nitrogen; Nitrogen - metabolism; Nitrogen Fixation; Nitrogenation; Protein interaction; Protein Interaction Maps; protein-protein interaction; Proteins; Proteome; Proteomes; rhizobia; Rhizobium - physiology; Root Nodules, Plant - genetics; Root Nodules, Plant - metabolism; Signal transduction; Symbiosis; Transcriptome; Transcriptomes
• ISSN: 1422-0067; 1661-6596; 1422-0067
• DOI: 10.3390/ijms222111907

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. Details about the molecular mechanisms of the communication and coordination between rhizobia and host plants is becoming clearer. For more systematic insights, there is an increasing demand for new studies integrating multiomics information. Here, we present a comprehensive computational framework integrating the reconstructed protein interactome of 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 USDA110 by computational approaches. Based on the comparison of interactomes between USDA110 and other rhizobia, we inferred that the slow growth of USDA110 may be due to the requirement of more protein modifications, and we 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 nine novel functional modules and eleven key protein hubs playing key roles in symbiosis were identified. The reconstructed interactome of USDA110 may serve as a valuable reference for studying the mechanism underlying the SNF system of rhizobia and legumes.