Basler Georg
Department of Environmental Protection, Estación Experimental del Zaidín, Consejo Superior de Investigaciones Científicas (CSIC), Profesor Albareda 1, 18008, Granada, Spain,
Methods Mol Biol. 2015;1279:183-204. doi: 10.1007/978-1-4939-2398-4_12.
In this chapter, we describe the application of constraint-based modeling to predict the impact of gene deletions on a metabolic phenotype. The metabolic reactions taking place inside cells form large networks, which have been reconstructed at a genome-scale for several organisms at increasing levels of detail. By integrating mathematical modeling techniques with biochemical principles, constraint-based approaches enable predictions of metabolite fluxes and growth under specific environmental conditions or for genetically modified microorganisms. Similar to the experimental knockout of a gene, predicting the essentiality of a metabolic gene for a phenotype further allows to generate hypotheses on its biological function and design of genetic engineering strategies for biotechnological applications. Here, we summarize the principles of constraint-based approaches and provide a detailed description of the procedure to predict the essentiality of metabolic genes with respect to a specific metabolic function. We exemplify the approach by predicting the essentiality of reactions in the citric acid cycle for the production of glucose from fatty acids.
在本章中，我们描述了基于约束的建模方法在预测基因缺失对代谢表型影响方面的应用。细胞内发生的代谢反应构成了庞大的网络，目前已针对多种生物体，以越来越详细的程度在基因组规模上进行了重建。通过将数学建模技术与生化原理相结合，基于约束的方法能够预测特定环境条件下或基因改造微生物中的代谢物通量和生长情况。与基因的实验性敲除类似，预测代谢基因对于某一表型的必要性，还能够进一步生成关于其生物学功能的假设，并设计用于生物技术应用的基因工程策略。在此，我们总结基于约束的方法的原理，并详细描述预测代谢基因对于特定代谢功能的必要性的程序。我们通过预测柠檬酸循环中反应对于从脂肪酸生产葡萄糖的必要性来举例说明该方法。
