Department of Bioengineering, University of California, 9500 Gilman Drive #0412, San Diego, La Jolla, CA 92093-0412, USA.
Metab Eng. 2010 May;12(3):173-86. doi: 10.1016/j.ymben.2009.10.003. Epub 2009 Oct 17.
Integrated approaches utilizing in silico analyses will be necessary to successfully advance the field of metabolic engineering. Here, we present an integrated approach through a systematic model-driven evaluation of the production potential for the bacterial production organism Escherichia coli to produce multiple native products from different representative feedstocks through coupling metabolite production to growth rate. Designs were examined for 11 unique central metabolism and amino acid targets from three different substrates under aerobic and anaerobic conditions. Optimal strain designs were reported for designs which possess maximum yield, substrate-specific productivity, and strength of growth-coupling for up to 10 reaction eliminations (knockouts). In total, growth-coupled designs could be identified for 36 out of the total 54 conditions tested, corresponding to eight out of the 11 targets. There were 17 different substrate/target pairs for which over 80% of the theoretical maximum potential could be achieved. The developed method introduces a new concept of objective function tilting for strain design. This study provides specific metabolic interventions (strain designs) for production strains that can be experimentally implemented, characterizes the potential for E. coli to produce native compounds, and outlines a strain design pipeline that can be utilized to design production strains for additional organisms.
利用计算分析的综合方法将是成功推进代谢工程领域的必要条件。在这里，我们通过系统的模型驱动评估提出了一种综合方法，该方法通过将代谢产物的产生与生长速率耦合，来评估细菌生产生物大肠杆菌从不同代表性原料生产多种天然产物的生产潜力。在需氧和厌氧条件下，针对来自三种不同底物的 11 个独特中心代谢物和氨基酸目标进行了设计研究。针对具有最大产率、底物特异性生产率和生长耦合强度的设计报告了最佳菌株设计，最高可达 10 个反应消除（敲除）。在总共测试的 54 种条件中，总共可以确定 36 种生长耦合设计，对应于 11 个目标中的 8 个。对于超过 80%的理论最大潜力可以实现的 17 个不同的底物/目标对，存在 17 个不同的底物/目标对。开发的方法为生产菌株引入了一种新的目标函数倾斜的菌株设计概念。本研究为生产菌株提供了具体的代谢干预（菌株设计），这些设计可以通过实验实施，描述了大肠杆菌生产天然化合物的潜力，并概述了可以用于设计其他生物生产菌株的菌株设计管道。
