Grupo de Bioprocesos, Instituto de Biología, Universidad de Antioquia, Calle 70 No. 52-21, Medellín, Colombia.
Department of Microbial Sciences, School of Biosciences and Medicine, University of Surrey, Guildford, Surrey, GU2 7XH, UK.
Bioprocess Biosyst Eng. 2018 May;41(5):657-669. doi: 10.1007/s00449-018-1900-9. Epub 2018 Feb 5.
In this work, we expanded and updated a genome-scale metabolic model of Streptomyces clavuligerus. The model includes 1021 genes and 1494 biochemical reactions; genome-reaction information was curated and new features related to clavam metabolism and to the biomass synthesis equation were incorporated. The model was validated using experimental data from the literature and simulations were performed to predict cellular growth and clavulanic acid biosynthesis. Flux balance analysis (FBA) showed that limiting concentrations of phosphate and an excess of ammonia accumulation are unfavorable for growth and clavulanic acid biosynthesis. The evaluation of different objective functions for FBA showed that maximization of ATP yields the best predictions for cellular behavior in continuous cultures, while the maximization of growth rate provides better predictions for batch cultures. Through gene essentiality analysis, 130 essential genes were found using a limited in silico media, while 100 essential genes were identified in amino acid-supplemented media. Finally, a strain design was carried out to identify candidate genes to be overexpressed or knocked out so as to maximize antibiotic biosynthesis. Interestingly, potential metabolic engineering targets, identified in this study, have not been tested experimentally.
在这项工作中，我们扩展和更新了链霉菌的基因组规模代谢模型。该模型包括 1021 个基因和 1494 个生化反应；对基因组-反应信息进行了整理，并纳入了与克拉维酸代谢和生物量合成方程相关的新特征。使用文献中的实验数据对模型进行了验证，并进行了模拟以预测细胞生长和克拉维酸生物合成。通量平衡分析（FBA）表明，磷酸盐的限制浓度和氨的积累过剩不利于生长和克拉维酸生物合成。对不同 FBA 目标函数的评估表明，最大化 ATP 产量可对连续培养中的细胞行为进行最佳预测，而最大生长速率可对分批培养进行更好的预测。通过基因必需性分析，在有限的计算机介质中发现了 130 个必需基因，而在添加氨基酸的介质中鉴定了 100 个必需基因。最后，进行了菌株设计以确定候选基因，以便进行过表达或敲除，从而最大限度地提高抗生素生物合成。有趣的是，本研究中确定的潜在代谢工程靶点尚未进行实验测试。
