title: Construction and analysis of a genome-scale metabolic network for Bacillus licheniformis WX-02.
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.
authors.affiliation: Agricultural Bioinformatics Key Laboratory of Hubei Province, College of Informatics, Huazhong Agricultural University, Wuhan 430070, PR China. Electronic address: gj30501@163.com.
authors.forename: Jing
authors.initials: J
authors.lastname: Guo
authors.affiliation: Agricultural Bioinformatics Key Laboratory of Hubei Province, College of Informatics, Huazhong Agricultural University, Wuhan 430070, PR China. Electronic address: 499946534@qq.com.
authors.forename: Hong
authors.initials: H
authors.lastname: Zhang
authors.affiliation: Agricultural Bioinformatics Key Laboratory of Hubei Province, College of Informatics, Huazhong Agricultural University, Wuhan 430070, PR China. Electronic address: wangchengmandy@126.com.
authors.forename: Cheng
authors.initials: C
authors.lastname: Wang
authors.affiliation: Agricultural Bioinformatics Key Laboratory of Hubei Province, College of Informatics, Huazhong Agricultural University, Wuhan 430070, PR China. Electronic address: longkaichang@163.com.
authors.forename: Ji-Wei
authors.initials: JW
authors.lastname: Chang
authors.affiliation: Agricultural Bioinformatics Key Laboratory of Hubei Province, College of Informatics, Huazhong Agricultural University, Wuhan 430070, PR China. Electronic address: llchen@mail.hzau.edu.cn.
authors.forename: Ling-Ling
authors.initials: LL
authors.lastname: Chen
mesh_terms: D000069976:Bacillus licheniformis / Q000235:genetics* / Q000378:metabolism*; D016680:Genome, Bacterial; D064688:Metabolic Flux Analysis; D053858:Metabolic Networks and Pathways / Q000235:genetics*; D046228:Microarray Analysis
keywords: Bacillus licheniformis WX-02; Flux balance analysis; Metabolic network; Phenotype microarray; Poly-γ-glutamic acid