Institute for Biotechnology and Bioengineering, University of Minho, Braga, Portugal.
PLoS One. 2013 Apr 23;8(4):e61648. doi: 10.1371/journal.pone.0061648. Print 2013.
Identification of optimal genetic manipulation strategies for redirecting substrate uptake towards a desired product is a challenging task owing to the complexity of metabolic networks, esp. in terms of large number of routes leading to the desired product. Algorithms that can exploit the whole range of optimal and suboptimal routes for product formation while respecting the biological objective of the cell are therefore much needed. Towards addressing this need, we here introduce the notion of structural flux, which is derived from the enumeration of all pathways in the metabolic network in question and accounts for the contribution towards a given biological objective function. We show that the theoretically estimated structural fluxes are good predictors of experimentally measured intra-cellular fluxes in two model organisms, namely, Escherichia coli and Saccharomyces cerevisiae. For a small number of fluxes for which the predictions were poor, the corresponding enzyme-coding transcripts were also found to be distinctly regulated, showing the ability of structural fluxes in capturing the underlying regulatory principles. Exploiting the observed correspondence between in vivo fluxes and structural fluxes, we propose an in silico metabolic engineering approach, iStruF, which enables the identification of gene deletion strategies that couple the cellular biological objective with the product flux while considering optimal as well as sub-optimal routes and their efficiency.
确定将底物摄取重新导向所需产物的最佳遗传操作策略是一项具有挑战性的任务，这是由于代谢网络的复杂性，特别是在通往所需产物的大量途径方面。因此，非常需要能够利用产品形成的所有最优和次优途径，同时尊重细胞的生物学目标的算法。为了解决这一需求，我们在这里引入了结构通量的概念，它是从所研究的代谢网络中所有途径的枚举中得出的，并考虑了对给定生物学目标函数的贡献。我们表明，理论上估计的结构通量是两种模式生物，即大肠杆菌和酿酒酵母中实验测量的细胞内通量的良好预测因子。对于预测效果较差的少数通量，相应的酶编码转录物也被发现明显受到调节，表明结构通量能够捕捉到潜在的调节原理。利用观察到的体内通量与结构通量之间的对应关系，我们提出了一种计算代谢工程方法 iStruF，该方法能够确定基因缺失策略，这些策略将细胞生物学目标与产物通量相耦合，同时考虑最优和次优途径及其效率。
