Papin Jason A, Price Nathan D, Palsson Bernhard Ø
Department of Bioengineering, University of California, San Diego, La Jolla, California 92093, USA.
Genome Res. 2002 Dec;12(12):1889-900. doi: 10.1101/gr.327702.
Extreme pathways are a unique and minimal set of vectors that completely characterize the steady-state capabilities of genome-scale metabolic networks. A framework is provided to mathematically characterize extreme pathway length and to study how individual reactions participate in the extreme pathway structure of a network. The length of an extreme pathway is the number of reactions that comprise it. Reaction participation is the percentage of extreme pathways that utilize a given reaction. These properties were computed for the production of individual amino acids and protein production in Helicobacter pylori and individual amino acid production in Haemophilus influenzae. Reaction participation classifies the reactions into groups that are always, sometimes, or never utilized for the production of a target product. The utilized reactions can be further grouped into correlated subsets of reactions, some of which are non-obvious, and which may, in turn, suggest regulatory structure. The length of the extreme pathways did not correlate with product yield or chemical complexity. The distributions of extreme pathway lengths in H. pylori were also very different from those in H. influenzae, showing a distinct systemic difference between the two organisms, despite overall similar metabolic networks. Reaction participation and extreme pathway lengths thus serve to elucidate systemic biological features.
极端途径是一组独特且最小的向量，它们完全表征了基因组规模代谢网络的稳态能力。提供了一个框架，用于从数学上表征极端途径长度，并研究单个反应如何参与网络的极端途径结构。极端途径的长度是构成它的反应数量。反应参与度是利用给定反应的极端途径的百分比。针对幽门螺杆菌中单个氨基酸的产生、蛋白质产生以及流感嗜血杆菌中单个氨基酸的产生计算了这些属性。反应参与度将反应分为总是、有时或从不用于产生目标产物的组。所利用的反应可以进一步分组为相关的反应子集，其中一些并不明显，这反过来可能暗示调控结构。极端途径的长度与产物产量或化学复杂性无关。幽门螺杆菌中极端途径长度的分布也与流感嗜血杆菌中的非常不同，尽管总体代谢网络相似，但显示出这两种生物体之间明显的系统差异。因此，反应参与度和极端途径长度有助于阐明系统生物学特征。
