An enhanced genome-scale metabolic reconstruction of Streptomyces clavuligerus identifies novel strain improvement strategies.
An enhanced genome-scale metabolic reconstruction of Streptomyces clavuligerus identifies novel strain improvement strategies.
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棒状链霉菌的基因组规模代谢重建增强确定了新的菌株改良策略。
DOI：
10.1007/s00449-018-1900-9
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发表时间：
2018
影响因子：
3.8
通讯作者：
Toro L
中科院分区：
文献类型：
--
作者：
Toro L
在这项工作中，我们扩展和更新了一个基因组规模的代谢模型链霉菌clavuligerus。该模型包括1021个基因和1494个生化反应;整理了基因组反应信息，并纳入了与克拉维代谢和生物质合成方程相关的新特征。使用文献中的实验数据验证该模型，并进行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，限制浓度的磷酸盐和过量的氨积累是不利的生长和克拉维酸的生物合成。FBA的不同目标函数的评价表明，ATP的最大化产生的细胞行为在连续培养的最佳预测，而生长速率的最大化提供了更好的预测分批培养。通过基因必要性分析，在有限的电子培养基中发现了130个必需基因，而在氨基酸补充培养基中发现了100个必需基因。最后，进行菌株设计以鉴定待过表达或敲除的候选基因，从而使抗生素生物合成最大化。有趣的是，本研究中确定的潜在代谢工程靶标尚未经过实验测试。
In this work, we expanded and updated a genome-scale metabolic model ofStreptomyces 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.