Construction and analysis of a genome-scale metabolic network for Bacillus licheniformis WX-02 |
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| Affiliation: | 1. Department of Zoology, Faculty of Science, Kasetsart University, Bangkok 10900, Thailand;2. Center for Systems Biology, Soochow University, Suzhou 215006, China;3. Biological Engineering Program, Faculty of Engineering, King Mongkut''s University of Technology Thonburi, 126 Pracha Uthit Rd, Thung Khru, Bangkok 10140, Thailand;4. Systems Biology Research Group, King Mongkut''s University of Technology Thonburi, Bangkok 10140, Thailand;5. Department of Chemical Engineering, Faculty of Engineering, King Mongkut''s University of Technology Thonburi, Bangkok 10140, Thailand;6. Bioprocess Technology Laboratory, National Center for Genetic Engineering and Biotechnology, National Sciences and Technology Development Agency, Khong Luang, Pathum Thani 12120, Thailand;7. Computational Biomodelling Laboratory for Agricultural Science and Technology, Faculty of Science, Kasetsart University, Bangkok 10900, Thailand |
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| Abstract: | We constructed the genome-scale metabolic network of Bacillus licheniformis (B. licheniformis) WX-02 by combining genomic annotation, high-throughput phenotype microarray (PM) experiments and literature-based metabolic information. The accuracy of the metabolic network was assessed by an OmniLog PM experiment. The final metabolic model iWX1009 contains 1009 genes, 1141 metabolites and 1762 reactions, and the predicted metabolic phenotypes showed an agreement rate of 76.8% with experimental PM data. In addition, key metabolic features such as growth yield, utilization of different substrates and essential genes were identified by flux balance analysis. A total of 195 essential genes were predicted from LB medium, among which 149 were verified with the experimental essential gene set of B. subtilis 168. With the removal of 5 reactions from the network, pathways for poly-γ-glutamic acid (γ-PGA) synthesis were optimized and the γ-PGA yield reached 83.8 mmol/h. Furthermore, the important metabolites and pathways related to γ-PGA synthesis and bacterium growth were comprehensively analyzed. The present study provides valuable clues for exploring the metabolisms and metabolic regulation of γ-PGA synthesis in B. licheniformis WX-02. |
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| Keywords: | Metabolic network Flux balance analysis Phenotype microarray Poly-γ-glutamic acid |
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