Abstract
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 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 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 B. diazoefficiens USDA110 may serve as a valuable reference for studying the mechanism underlying the SNF system of rhizobia and legumes.
Highlights
Introduction published maps and institutional affilIn most cases, rhizobia are a group of Gram-negative soil bacteria within the familyRhizobiaceae
A part of domaindomain interaction (DDI) were inferred from experimental protein-protein interaction (PPI) in databases based on domain sequences with score > 0.5, and another part of DDIs were obtained from 3DID database based on the domain structure with score > 0
The PPIs in B. diazoefficiens USDA110 were predicted by integration of an “Interolog”
Summary
An “interolog” is a conserved interaction between a pair of proteins which have interacting homologs in another organism [34,35]. USDA110, if their homologous proteins in other species have an interaction, they are predicted to be interacting. For the “Interolog” method, we selected six prokaryotes as primary reference species including Campylobacter jejuni, Escherichia coli, Helicobacter pylori, Mesorhizobium loti, Synechocystis sp. All protein sequences of B. diazoefficiens USDA110 and of the six reference species were downloaded from the NCBI RefSeq database. We predicted PPIs of B. diazoefficiens USDA110 by the “Interolog”. Protein sequences of the six reference species were prepared to do homologous alignment with B. diazoefficiens USDA110, and on the other hand, experimental PPIs and their protein sequences from BioGRID [42], DIP [43], IntAct [44]. The homologous proteins were acquired by using InParanoid [46] (version 4.1) under default parameters
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