title: Genome-scale reconstruction of a metabolic network for Gluconobacter oxydans 621H.
abstract: Gluconobacter oxydans is a Gram-negative bacterium with a number of biotechnological applications. Although the genome of G. oxydans has been reported in 2005, the systematical cellular metabolism in this high-value bacterium, however, remains unclear. In this study, a genome-scale metabolic network of G. oxydans 621H, iXW433, was reconstructed and validated on the basis of the known genome annotations and biochemical information. This reconstructed model included 433 genes, 859 reactions, and 985 metabolites. To test the capability of the model, gene and reaction essentiality analysis, flux variability analysis, and robustness analysis simulations were performed. The metabolic states predicted by the model were highly consistent with the experimental data of G. oxydans. According to the result, 92 genes and 137 reactions were identified to be essential, 194 reactions were found to be variable by flux variability analysis, and 2 possible genetically modified targets were determined. The model would be valuable for further research on G. oxydans and thereby expanding its application.
authors.affiliation: Department of Biological Engineering and Key Laboratory of Systems Bioengineering of the Ministry of Education, School of Chemical Engineering and Technology, Tianjin University, Tianjin 300072, China.
authors.forename: Xinsen
authors.initials: X
authors.lastname: Wu
authors.affiliation: Department of Biological Engineering and Key Laboratory of Systems Bioengineering of the Ministry of Education, School of Chemical Engineering and Technology, Tianjin University, Tianjin 300072, China.
authors.forename: Xiaoyang
authors.initials: X
authors.lastname: Wang
authors.affiliation: Department of Biological Engineering and Key Laboratory of Systems Bioengineering of the Ministry of Education, School of Chemical Engineering and Technology, Tianjin University, Tianjin 300072, China. Electronic address: wenyulu@tju.edu.cn.
authors.forename: Wenyu
authors.initials: W
authors.lastname: Lu
mesh_terms: D001426:Bacterial Proteins / Q000235:genetics*; D049109:Cell Proliferation; D002874:Chromosome Mapping; D003198:Computer Simulation; D015964:Gene Expression Regulation, Bacterial / Q000235:genetics; D016680:Genome, Bacterial / Q000235:genetics*; D020600:Gluconobacter oxydans / Q000235:genetics*; D005990:Glycerol / Q000378:metabolism*; D064688:Metabolic Flux Analysis; D055442:Metabolome / Q000235:genetics*; D008957:Models, Genetic
chemical_list: D001426:Bacterial Proteins; D005990:Glycerol
keywords: Flux balance analysis; Flux variability analysis; Gene essentiality analysis; Genome-scale metabolic network; Gluconobacter oxydans