Comparative analysis of active networks reveals the changes of key proteins and their interactions under different oxygen levels in Shewanella oneidensis MR-1

Abstract

Purpose: The extracellular electron transfer (EET) capability enables electroactive microorganisms have a wide range of applications in energy production, wastewater treatment, bioremediation and chemical synthesis. Because the oxygen levels will sharply affect the EET process, we integrated transcriptome changes under different oxygen levels with protein–protein interaction (PPI) network to study the specific changes under these conditions in a typical electroactive microorganism Shewanella oneidensis MR-1 (S. oneidensis MR-1). Methods: First, the mRNA expression data of S. oneidensis MR-1 under different oxygen levels were integrated into its PPI network to construct the active protein networks. Then, we studied the changes of key proteins and their interactions by comparative analysis of multiple pairs of active networks. Results: The analysis of node centrality and its changes in the active networks under high and low oxygen levels shows that most of the key nodes in the network are ribosomes or proteins closely related to ribosomes. The results of our centrality versus centrality change analysis of nodes show that the two proteins FlgB and PetA are the largest changed proteins. Among these proteins, the FlgB protein is the structural component of flagella, while PetA protein is closely related to cytochrome c. Furthermore, we also analyzed the changes in protein–protein interactions in the active networks under different oxygen levels, identified the key interactions in each pair of active networks, and finally screened out the key interaction Tig-RplX that exists in three pairs of active networks. Conclusion: Our results indicate that the translational processes of proteins and the corresponding translation efficiency may play an important role before and after the activation of the EET process of S. oneidensis MR-1. Furthermore, this study can also provide some guidance for identifying key proteins and interactions under different conditions for this species.