Genome-Scale Modeling of Light-Driven Reductant Partitioning and Carbon Fluxes in Diazotrophic Unicellular Cyanobacterium Cyanothece sp. ATCC 51142

Genome-scale metabolic models have proven useful for answering fundamental questions about metabolic capabilities of a variety of microorganisms, as well as informing their metabolic engineering. However, only a few models are available for oxygenic photosynthetic microorganisms, particularly in cyanobacteria in which photosynthetic and respiratory electron transport chains (ETC) share components. We addressed the complexity of cyanobacterial ETC by developing a genome-scale model for the diazotrophic cyanobacterium, Cyanothece sp. ATCC 51142. The resulting metabolic reconstruction, iCce806, consists of 806 genes associated with 667 metabolic reactions and includes a detailed representation of the ETC and a biomass equation based on experimental measurements. Both computational and experimental approaches were used to investigate light-driven metabolism in Cyanothece sp. ATCC 51142, with a particular focus on reductant production and partitioning within the ETC. The simulation results suggest that growth and metabolic flux distributions are substantially impacted by the relative amounts of light going into the individual photosystems. When growth is limited by the flux through photosystem I, terminal respiratory oxidases are predicted to be an important mechanism for removing excess reductant. Similarly, under photosystem II flux limitation, excess electron carriers must be removed via cyclic electron transport. Furthermore, in silico calculations were in good quantitative agreement with the measured growth rates whereas predictions of reaction usage were qualitatively consistent with protein and mRNA expression data, which we used to further improve the resolution of intracellular flux values.

基因组规模代谢模型（Genome-scale metabolic models）已被证实可用于解答各类微生物代谢能力相关的基础科学问题，同时可为其代谢工程研究提供指导。然而目前针对产氧光合微生物的此类模型仍较为稀缺，针对蓝细菌的模型更是寥寥无几——蓝细菌的光合电子传递链与呼吸电子传递链（ETC）共享部分组分。为解决蓝细菌ETC的构建复杂性，本研究针对固氮蓝细菌*Cyanothece sp. ATCC 51142*构建了基因组规模代谢模型。本研究构建的代谢重建模型iCce806包含806个关联基因与667个代谢反应，详细刻画了ETC的组分，并基于实验测量数据构建了生物量方程。本研究结合计算与实验两种手段，探究了*Cyanothece sp. ATCC 51142*的光驱动代谢过程，重点关注了还原剂的生成与在ETC内的分配情况。模拟结果表明，分配至各光系统的相对光强会显著影响菌株生长与代谢流分布。当菌株生长受到光系统I电子传递流限制时，终端呼吸氧化酶被预测为清除过量还原剂的关键机制。类似地，当生长受光系统II电子传递流限制时，过量电子载体需通过循环电子传递途径进行清除。此外，计算机模拟（in silico）计算结果与实测生长速率具有良好的定量一致性；而关于反应利用情况的预测结果在定性层面与蛋白质及mRNA表达数据相符，本研究据此进一步提升了胞内代谢流值的解析精度。