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Background   Zymomonas mobilis  ZM4 is a Gram-negative bacterium that can efficiently produce ethanol from various carbon substrates, including glucose, fructose, and sucrose,  via  the Entner-Doudoroff pathway. However, systems metabolic engineering is required to further enhance its metabolic performance for industrial application. As an important step towards this goal, the genome-scale metabolic model of  Z. mobilis  is required to systematically analyze  in silico  the metabolic characteristics of this bacterium under a wide range of genotypic and environmental conditions.    Results  The genome-scale metabolic model of  Z. mobilis  ZM4, ZmoMBEL601, was reconstructed based on its annotated genes, literature, physiological and biochemical databases. The metabolic model comprises 579 metabolites and 601 metabolic reactions (571 biochemical conversion and 30 transport reactions), built upon extensive search of existing knowledge. Physiological features of  Z. mobilis  were then examined using constraints-based flux analysis in detail as follows. First, the physiological changes of  Z. mobilis  as it shifts from anaerobic to aerobic environments (i.e. aerobic shift) were investigated. Then the intensities of flux-sum, which is the cluster of either all ingoing or outgoing fluxes through a metabolite, and the maximum  in silico  yields of ethanol for  Z. mobilis  and  Escherichia coli  were compared and analyzed. Furthermore, the substrate utilization range of  Z. mobilis  was expanded to include pentose sugar metabolism by introducing metabolic pathways to allow  Z. mobilis  to utilize pentose sugars. Finally, double gene knock-out simulations were performed to design a strategy for efficiently producing succinic acid as another example of application of the genome-scale metabolic model of  Z. mobilis .    Conclusion  The genome-scale metabolic model reconstructed in this study was able to successfully represent the metabolic characteristics of  Z. mobilis  under various conditions as validated by experiments and literature information. This reconstructed metabolic model will allow better understanding of  Z. mobilis  metabolism and consequently designing metabolic engineering strategies for various biotechnological applications.

microbial cell factories

The genome-scale metabolic network analysis of Zymomonas mobilis ZM4 explains physiological features and suggests ethanol and succinic acid production strategies