Metabolic network reconstruction and flux variability analysis of storage synthesis in developing oilseed rape (Brassica napus L.) embryos
Metabolic network reconstruction and flux variability analysis of storage synthesis in developing oilseed rape (Brassica napus L.) embryos
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DOI：
10.1111/j.1365-313x.2011.04613.x
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发表时间：
2011-08-01
期刊：
影响因子：
7.2
通讯作者：
Schwender, Joerg
中科院分区：
文献类型：
--
作者：
Hay, Jordan;Schwender, Joerg
大规模生物化学网络的计算模拟可用于分析和预测生物体的代谢行为，例如发育中的种子。基于生物化学文献、途径数据库和决定反应方向的规则，我们重建了一个代表油菜种子贮藏代谢的化学计量代谢网络模型bna572。在高度区室化的网络中，572个反应中约有25%是将9个亚细胞区室与环境相互连接的运输反应。根据已知的生理能力发展B。以油菜胚为材料，定义了四种营养条件来模拟异养或光异养，每种营养条件都与无机氮（氨、硝酸盐）或氨基酸作为氮源的可用性相结合。基于数学线性优化的最优解空间进行了全面的探索，通过通量变异性分析，从而确定每个反应的最优下允许的通量值的范围。然后将通量值的范围和可变性分类为通量可变性类型。在四种营养条件下，大约13%的反应具有可变的通量值，10 - 11%是可替代的（可以是无活性的），这两种反应都表明代谢冗余，例如，通过同工酶，亚细胞区室化或替代途径的存在。大约三分之一的反应从未使用过，并且与储存合成的次优途径有关。57个反应在不同营养条件下改变通量变异类型，表明它们在代谢调节中的作用。该预测建模框架允许分析和定量探索发育中的B的储存代谢。油菜籽
Computational simulation of large-scale biochemical networks can be used to analyze and predict the metabolic behavior of an organism, such as a developing seed. Based on the biochemical literature, pathways databases and decision rules defining reaction directionality we reconstructed bna572, a stoichiometric metabolic network model representing Brassica napus seed storage metabolism. In the highly compartmentalized network about 25% of the 572 reactions are transport reactions interconnecting nine subcellular compartments and the environment. According to known physiological capabilities of developing B. napus embryos, four nutritional conditions were defined to simulate heterotrophy or photoheterotrophy, each in combination with the availability of inorganic nitrogen (ammonia, nitrate) or amino acids as nitrogen sources. Based on mathematical linear optimization the optimal solution space was comprehensively explored by flux variability analysis, thereby identifying for each reaction the range of flux values allowable under optimality. The range and variability of flux values was then categorized into flux variability types. Across the four nutritional conditions, approximately 13% of the reactions have variable flux values and 10-11% are substitutable (can be inactive), both indicating metabolic redundancy given, for example, by isoenzymes, subcellular compartmentalization or the presence of alternative pathways. About one-third of the reactions are never used and are associated with pathways that are suboptimal for storage synthesis. Fifty-seven reactions change flux variability type among the different nutritional conditions, indicating their function in metabolic adjustments. This predictive modeling framework allows analysis and quantitative exploration of storage metabolism of a developing B. napus oilseed.