Waksman Institute, Rutgers University, New Brunswick, NJ 08901, USA.
Center for Computational and Integrative Biology, Rutgers University, Camden, NJ 08102, USA.
Biochim Biophys Acta Bioenerg. 2017 Apr;1858(4):276-287. doi: 10.1016/j.bbabio.2016.12.007. Epub 2016 Dec 22.
We have constructed and experimentally tested a comprehensive genome-scale model of photoautotrophic growth, denoted iSyp821, for the cyanobacterium Synechococcus sp. PCC 7002. iSyp821 incorporates a variable biomass objective function (vBOF), in which stoichiometries of the major biomass components vary according to light intensity. The vBOF was constrained to fit the measured cellular carbohydrate/protein content under different light intensities. iSyp821 provides rigorous agreement with experimentally measured cell growth rates and inorganic carbon uptake rates as a function of light intensity. iSyp821 predicts two observed metabolic transitions that occur as light intensity increases: 1) from PSI-cyclic to linear electron flow (greater redox energy), and 2) from carbon allocation as proteins (growth) to carbohydrates (energy storage) mode. iSyp821 predicts photoautotrophic carbon flux into 1) a hybrid gluconeogenesis-pentose phosphate (PP) pathway that produces glycogen by an alternative pathway than conventional gluconeogenesis, and 2) the photorespiration pathway to synthesize the essential amino acid, glycine. Quantitative fluxes through both pathways were verified experimentally by following the kinetics of formation of C metabolites from CO fixation. iSyp821 was modified to include changes in gene products (enzymes) from experimentally measured transcriptomic data and applied to estimate changes in concentrations of metabolites arising from nutrient stress. Using this strategy, we found that iSyp821 correctly predicts the observed redistribution pattern of carbon products under nitrogen depletion, including decreased rates of CO uptake, amino acid synthesis, and increased rates of glycogen and lipid synthesis.
我们构建并实验测试了一个综合的、基于基因组规模的蓝藻 Synechococcus sp. PCC 7002 的光自养生长模型，记为 iSyp821。iSyp821 包含一个可变生物质目标函数（vBOF），其中主要生物质成分的化学计量根据光强而变化。vBOF 被约束以拟合在不同光强下测量到的细胞碳水化合物/蛋白质含量。iSyp821 与实验测量的细胞生长速率和无机碳摄取速率随光强的变化严格一致。iSyp821 预测了两个随着光强增加而发生的观察到的代谢转变：1）从 PSI-循环到线性电子流（更多的氧化还原能量），2）从将碳分配为蛋白质（生长）转变为碳水化合物（能量储存）模式。iSyp821 预测光自养碳通量进入 1）一种杂种糖异生-戊糖磷酸（PP）途径，该途径通过不同于传统糖异生的替代途径产生糖原，2）光呼吸途径以合成必需氨基酸甘氨酸。通过追踪 CO 固定产生的 C 代谢物的动力学，实验验证了这两条途径的定量通量。我们修改了 iSyp821，纳入了从实验测量的转录组数据中获得的基因产物（酶）的变化，并应用于估计营养胁迫引起的代谢物浓度变化。使用这种策略，我们发现 iSyp821 正确预测了氮耗尽下碳产物的观察到的再分配模式，包括 CO 摄取、氨基酸合成和糖原和脂质合成的速率降低，以及速率增加。
