Fernández-Castané Alfred, Fehér Tamás, Carbonell Pablo, Pauthenier Cyrille, Faulon Jean-Loup
Institute of Systems and Synthetic Biology, University of Evry-Val-d'Essonne, CNRS FRE3561, Genopole(®) Campus 1, Genavenir 6, 5 rue Henri Desbruères, F-91030 Evry Cedex, France.
J Biotechnol. 2014 Dec 20;192 Pt B:302-13. doi: 10.1016/j.jbiotec.2014.03.029. Epub 2014 Apr 2.
The development and application of biotechnology-based strategies has had a great socio-economical impact and is likely to play a crucial role in the foundation of more sustainable and efficient industrial processes. Within biotechnology, metabolic engineering aims at the directed improvement of cellular properties, often with the goal of synthesizing a target chemical compound. The use of computer-aided design (CAD) tools, along with the continuously emerging advanced genetic engineering techniques have allowed metabolic engineering to broaden and streamline the process of heterologous compound-production. In this work, we review the CAD tools available for metabolic engineering with an emphasis, on retrosynthesis methodologies. Recent advances in genetic engineering strategies for pathway implementation and optimization are also reviewed as well as a range of bionalytical tools to validate in silico predictions. A case study applying retrosynthesis is presented as an experimental verification of the output from Retropath, the first complete automated computational pipeline applicable to metabolic engineering. Applying this CAD pipeline, together with genetic reassembly and optimization of culture conditions led to improved production of the plant flavonoid pinocembrin. Coupling CAD tools with advanced genetic engineering strategies and bioprocess optimization is crucial for enhanced product yields and will be of great value for the development of non-natural products through sustainable biotechnological processes.
基于生物技术的策略的发展与应用已产生了巨大的社会经济影响，并可能在更可持续、高效的工业生产过程的建立中发挥关键作用。在生物技术领域，代谢工程旨在定向改善细胞特性，其目标通常是合成目标化合物。计算机辅助设计（CAD）工具的应用，以及不断涌现的先进基因工程技术，使代谢工程能够拓宽并简化异源化合物的生产过程。在本文中，我们重点回顾了可用于代谢工程的CAD工具，特别是逆合成方法。同时，我们还回顾了基因工程策略在途径实施和优化方面的最新进展，以及一系列用于验证计算机模拟预测的生物分析工具。本文展示了一个应用逆合成的案例研究，作为Retropath（首个适用于代谢工程的完整自动化计算流程）输出结果的实验验证。应用此CAD流程，结合基因重组和培养条件优化，提高了植物类黄酮松属素的产量。将CAD工具与先进的基因工程策略及生物过程优化相结合，对于提高产品产量至关重要，并且对于通过可持续生物技术过程开发非天然产品具有重要价值。
