Reconstruction and analysis of Bacillus megaterium metabolic model based on literature study

Abstract:

Abstract:［Objective］ The aim of this study is to reconstruct the metabolic model of Bacillus megaterium by literature study，which would be used to elucidate physiological properties in detail and refine physiological functions． ［Methods］We built a literature database by searching B．megaterium related literatures from Web of Science，PubMed，United States Patent and Trademark Office (USPTO) Patent Databases，Derwent Innovations Index and China National Knowledge Infrastructure (CNKI)．Depending on this database，we extracted the functional genes，enzymes，metabolites and metabolic reactions (including transport reactions) through literature studies．Then，we filled gaps through KEGG Mapper and adding sink reactions．The operation of Matlab programs reconstructed the metabolic model (in the form of Systems Biology Markup Language) of B． megaterium． ［Results］ The refined metabolic network model contained 292 metabolic reactions，378 metabolites，220 enzymes and 217 genes． With the restrictive condition of 1.62 mmol/g cell/h of glucose uptake rate，the simulated specific growth rate was 0.089 h－1，a little lower than the experimental value 0.11 h－1. In addition，the accuracy of the single gene deletion simulation in pyrimidine metabolism reached 90%．［Conclusion］ The final metabolic network model covered the biochemical information of citrate cycle，glycolysis，pentose phosphate pathway，fatty acid metabolism，vitamin B12 biosynthesis and amino acid biosynthesis，and reflected the effect of substrates and genes on the growth of the bacterium to a certain extent．