Institute of Biochemistry and Biology, University of Potsdam, Karl-Liebknecht-Str. 24-25, D-14476 Potsdam, Germany.
Bioinformatics. 2012 Sep 15;28(18):i502-i508. doi: 10.1093/bioinformatics/bts381.
Metabolic engineering aims at modulating the capabilities of metabolic networks by changing the activity of biochemical reactions. The existing constraint-based approaches for metabolic engineering have proven useful, but are limited only to reactions catalogued in various pathway databases.
We consider the alternative of designing synthetic strategies which can be used not only to characterize the maximum theoretically possible product yield but also to engineer networks with optimal conversion capability by using a suitable biochemically feasible reaction called 'stoichiometric capacitance'. In addition, we provide a theoretical solution for decomposing a given stoichiometric capacitance over a set of known enzymatic reactions. We determine the stoichiometric capacitance for genome-scale metabolic networks of 10 organisms from different kingdoms of life and examine its implications for the alterations in flux variability patterns. Our empirical findings suggest that the theoretical capacity of metabolic networks comes at a cost of dramatic system's changes.
larhlimi@mpimp-golm.mpg.de, or nikoloski@mpimp-golm.mpg.de
Supplementary tables are available at Bioinformatics online.
代谢工程旨在通过改变生化反应的活性来调节代谢网络的能力。现有的代谢工程基于约束的方法已经被证明是有用的，但它们仅限于各种途径数据库中列出的反应。
我们考虑设计合成策略的替代方案，这些策略不仅可以用于表征最大理论可能的产物产率，还可以通过使用合适的生物化学可行反应“计量电容”来设计具有最佳转化能力的网络。此外，我们还提供了一种理论解决方案，用于将给定的计量电容分解为一组已知的酶反应。我们确定了来自不同生命王国的 10 种生物体的基因组规模代谢网络的计量电容，并研究了其对通量可变性模式变化的影响。我们的实证研究结果表明，代谢网络的理论容量是以系统剧烈变化为代价的。
larhlimi@mpimp-golm.mpg.de 或 nikoloski@mpimp-golm.mpg.de
补充表格可在生物信息学在线获得。
