Department of Microbial Biotechnology, School of Biology, College of Science, University of Tehran, Tehran, Iran.
Department of Biotechnology, College of Science, University of Tehran, Tehran, Iran.
Sci Rep. 2020 May 8;10(1):7782. doi: 10.1038/s41598-020-64721-x.
Zymomonas mobilis ZM4 has recently been used for a variety of biotechnological purposes. To rationally enhance its metabolic performance, a reliable genome-scale metabolic network model (GEM) of this organism is required. To this end, we reconstructed a genome-scale metabolic model (iHN446) for Z. mobilis, which involves 446 genes, 859 reactions, and 894 metabolites. We started by first reconciling the existing GEMs previously constructed for Z. mobilis to obtain a draft network. Next, recent gene annotations, up-to-date literature, physiological data and biochemical databases were used to upgrade the network. Afterward, the draft network went through a curative and iterative process of gap-filling by computational tools and manual refinement. The final model was evaluated using experimental data and literature information. We next applied this model as a platform for analyzing the links between transcriptome-flux and transcriptome-metabolome. We found that experimental observations were in agreement with the predicted results from our final GEM. Taken together, this comprehensive model (iHN446) can be utilized for studying metabolism in Z. mobilis and finding rational targets for metabolic engineering applications.
运动发酵单胞菌 ZM4 最近被用于各种生物技术目的。为了合理地提高其代谢性能，需要构建该生物体的可靠基因组尺度代谢网络模型（GEM）。为此，我们构建了运动发酵单胞菌的基因组尺度代谢模型（iHN446），其中涉及 446 个基因、859 个反应和 894 个代谢物。我们首先通过协调以前为运动发酵单胞菌构建的现有 GEM 来获得草案网络。接下来，使用最新的基因注释、最新的文献、生理数据和生化数据库来升级网络。此后，通过计算工具和手动细化对草案网络进行了修复和迭代过程。最终模型使用实验数据和文献信息进行了评估。我们接下来将该模型用作分析转录组通量和转录组代谢组之间联系的平台。我们发现，实验观察结果与我们最终 GEM 的预测结果一致。总之，这个全面的模型（iHN446）可用于研究运动发酵单胞菌的代谢，并找到代谢工程应用的合理目标。
