A Method of Accounting for Enzyme Costs in Flux Balance Analysis Reveals Alternative Pathways and Metabolite Stores in an Illuminated Arabidopsis Leaf
A Method of Accounting for Enzyme Costs in Flux Balance Analysis Reveals Alternative Pathways and Metabolite Stores in an Illuminated Arabidopsis Leaf
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DOI：
10.1104/pp.15.00880
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发表时间：
2015-11-01
期刊：
影响因子：
7.4
通讯作者：
Sweetlove, Lee J.
中科院分区：
文献类型：
--
作者：
Cheung, C. Y. Maurice;Ratcliffe, R. George;Sweetlove, Lee J.
植物代谢通量平衡分析是预测代谢通量表型和探索植物代谢网络在不同细胞类型、组织和时间阶段传递特定结果的方式的一种既定方法。一个反复出现的主题是需要探讨网络在实现其目标方面的灵活性，特别是确定替代途径在多大程度上有助于实现具体成果。不幸的是，传统通量平衡分析的预测最大限度地减少了可选路径的同时运行，但通过引入通量加权因子以允许支持每种通量的可变内在成本，可以在单个模拟中激活不同的路径，从而通过平均数千次模拟来探索可选路径。该方法已应用于拟南芥（Arabidopsis thaliana）叶片代谢的diel基因组尺度模型，以探索该网络在满足叶片在光照下代谢需求方面的灵活性。这一发现揭示了卡尔文-本森循环中可选择的通量模式，揭示了叶片中可选择的短暂碳储存的潜力，并预测了可选择的电子流途径和能量再平衡中无用循环的光依赖性贡献。该分析的显著特征包括碳水化合物和四碳有机酸作为短暂储存形式之间的光依赖性权衡，以及ATP和NADPH消耗的多种途径可以促进光合代谢需求与光子捕获可获得能量的平衡。
Flux balance analysis of plant metabolism is an established method for predicting metabolic flux phenotypes and for exploring the way in which the plant metabolic network delivers specific outcomes in different cell types, tissues, and temporal phases. A recurring theme is the need to explore the flexibility of the network in meeting its objectives and, in particular, to establish the extent to which alternative pathways can contribute to achieving specific outcomes. Unfortunately, predictions from conventional flux balance analysis minimize the simultaneous operation of alternative pathways, but by introducing flux weighting factors to allow for the variable intrinsic cost of supporting each flux, it is possible to activate different pathways in individual simulations and, thus, to explore alternative pathways by averaging thousands of simulations. This new method has been applied to a diel genome-scale model of Arabidopsis (Arabidopsis thaliana) leaf metabolism to explore the flexibility of the network in meeting the metabolic requirements of the leaf in the light. This identified alternative flux modes in the Calvin-Benson cycle revealed the potential for alternative transitory carbon stores in leaves and led to predictions about the light-dependent contribution of alternative electron flow pathways and futile cycles in energy rebalancing. Notable features of the analysis include the light-dependent tradeoff between the use of carbohydrates and four-carbon organic acids as transitory storage forms and the way in which multiple pathways for the consumption of ATP and NADPH can contribute to the balancing of the requirements of photosynthetic metabolism with the energy available from photon capture.