Exploring Extracellular Electron Transfer Mechanism Of Electricigens Based On Integrated Network Analysis

Microbial fuel cells are regarded as environmental friendly new energy sources, which utilize the electrochemical microorganisms to replace anodic metal catalysts. The electrochemical microorganisms refer to electricigens, which consume the substrate in the environment to accomplish the process that transfer electron the extracellular electron acceptor via cellular respiration. This paves the road of green energy research in order to take the place of traditional fossil fuels and eliminate the environmental issues which have bourht to us. Although this idea has been around for several years but, so far, microbial fuel cells have not been able to produce enough current to power even basic appliances, the low power output efficiency confines its industrialized application.Shewanella oneidensis MR-1 is a gram-negative and facultative anaerobic bacterium, which is considered as a kind of model organism in electricigens, owns the superior performance of growing in various substrates and the utilization of mutiple electron acceptor, In this study we chose it as research object, aiming to search for the key genes and reactions in order to reveal the mechanism of the extracellular electron transfer, meanwhile, providing guidance to improve the electron transport efficiency by means of genetic engineering and metabolic engineering, exploring the multiple omics analysis method to combine metabolic network and gene expression data in an integrated ways.Based on the gene annotation information of NCBI and protein metabolism information of KEGG database, we reconstructed the key electron mediator metabolic sub-network of S. oneidensis MR-1 using Merlin, a automated construction software. After mannual curation, the metabolic sub-network contains 38 reactions,44 genes and 76 metabolites. Compared with the genome scale metabolic network of iSO783 and iMR1₇99, they have 24 reactions in common. Compared with the riboflavin metabolism, ubiquinone and other terpenoid-quinone biosynthesis pathway in KEGG database, they have 6 and 8 reactions in common, respectively. The metabolic sub-network possesses the character of small-world and scaleless property via the analysis of networks topology. And those reactions involving quinones, as a significant electron mediator, account for the largest in the the reactions of metabolic sub-network.Genome scale metalbolic network analysis was employed. Based on Flux Balance Analysis and the COBRA Toolbox of Matlab, the MR1₇99 network by Ong et al. was taken for further investigation. Eight key biochemical reactions were found, including direct, indirect and flavin-related modes of electron transport. By comparison, only two of the eight reactions are not in the sub-network of electron mediator mentalism. The analysis of robustness shows that the electron transport and the growth rate are non-linearly dependent, implying that the growth rate of microbes should be under control for the purpose of.harvesting maximum electricity.Finally, genes in the electron mediator metallic sub-network were analyzed, from the perspective of gene expression, to predict potential pathway of extra-cellular electron transfer under specific condition or environment. By using the gene expression data from GEO database and the Bioconductor package which is based on the R language, the specificity of electron transport, key genes and reactions, under either anaerobic or aerobic conditions, was found. For instance, when in the lactate medium, the microbes employ the MtrABC pathway for the direct and indirect electron transfer under aerobic conditions, and use flavin-related pathways, cooperated with the DmsEF pathway, under anaerobic environments.The discovery of key genes and biochemical reactions has improved the understanding of the mechanism for extra-cellular electron transport of electricigens, and could guide further investigation of the culture of efficient electricigen strains, by genetic and metallic engineering.