BIOMATH, Dept. of Applied Mathematics, Biometrics, and Process Control, Ghent University, Ghent 9000, Belgium.
Biotechnol Prog. 2010 Mar-Apr;26(2):313-31. doi: 10.1002/btpr.349.
The state of the art tools for modeling metabolism, typically used in the domain of metabolic engineering, were reviewed. The tools considered are stoichiometric network analysis (elementary modes and extreme pathways), stoichiometric modeling (metabolic flux analysis, flux balance analysis, and carbon modeling), mechanistic and approximative modeling, cybernetic modeling, and multivariate statistics. In the context of metabolic engineering, one should be aware that the usefulness of these tools to optimize microbial metabolism for overproducing a target compound depends predominantly on the characteristic properties of that compound. Because of their shortcomings not all tools are suitable for every kind of optimization; issues like the dependence of the target compound's synthesis on severe (redox) constraints, the characteristics of its formation pathway, and the achievable/desired flux towards the target compound should play a role when choosing the optimization strategy.
本文综述了用于代谢建模的先进工具，这些工具通常用于代谢工程领域。所考虑的工具包括化学计量网络分析（基本模式和极端途径）、化学计量建模（代谢通量分析、通量平衡分析和碳建模）、机理和近似建模、控制论建模和多元统计。在代谢工程的背景下，应该意识到，这些工具对于优化微生物代谢以过度生产目标化合物的有用性主要取决于该化合物的特征性质。由于它们的缺点，并非所有工具都适用于每种类型的优化；在选择优化策略时，应考虑目标化合物合成对严重（氧化还原）约束、其形成途径的特征以及目标化合物的可实现/期望通量等问题。
