Genome-Scale Model Reveals Metabolic Basis of Biomass Partitioning in a Model Diatom

Diatoms are eukaryotic microalgae that contain genes from various sources, including bacteria and the secondary endosymbiotic host. Due to this unique combination of genes, diatoms are taxonomically and functionally distinct from other algae and vascular plants and confer novel metabolic capabilities. Based on the genome annotation, we performed a genome-scale metabolic network reconstruction for the marine diatom Phaeodactylum tricornutum. Due to their endosymbiotic origin, diatoms possess a complex chloroplast structure which complicates the prediction of subcellular protein localization. Based on previous work we implemented a pipeline that exploits a series of bioinformatics tools to predict protein localization. The manually curated reconstructed metabolic network iLB1027_lipid accounts for 1,027 genes associated with 4,456 reactions and 2,172 metabolites distributed across six compartments. To constrain the genome-scale model, we determined the organism specific biomass composition in terms of lipids, carbohydrates, and proteins using Fourier transform infrared spectrometry. Our simulations indicate the presence of a yet unknown glutamine-ornithine shunt that could be used to transfer reducing equivalents generated by photosynthesis to the mitochondria. The model reflects the known biochemical composition of P. tricornutum in defined culture conditions and enables metabolic engineering strategies to improve the use of P. tricornutum for biotechnological applications.硅藻是一类携带来自多种来源基因的真核微藻类，其基因来源包括细菌与次生内共生宿主。由于这种独特的基因组合，硅藻在分类学与功能学层面均区别于其他藻类与维管植物，并赋予了全新的代谢能力。基于基因组注释结果，我们针对海洋硅藻三角褐指藻（Phaeodactylum tricornutum）开展了基因组规模代谢网络重构。由于其起源于内共生事件，硅藻拥有复杂的叶绿体结构，这给亚细胞蛋白质定位预测带来了挑战。基于既往研究，我们搭建了一套整合一系列生物信息学工具的流程以预测蛋白质定位。经人工整理的代谢网络iLB1027_lipid涵盖了1027个基因，关联4456个反应与2172个代谢物，分布于6个亚细胞区室。为约束该基因组规模模型，我们采用傅里叶变换红外光谱法测定了该物种特异性的生物质组成，包括脂质、碳水化合物与蛋白质。模拟结果显示，存在一条此前未被报道的谷氨酰胺-鸟氨酸旁路途径，该途径可用于将光合作用产生的还原当量转运至线粒体。该模型能够反映三角褐指藻在限定培养条件下的已知生化组成，并可为通过代谢工程手段提升三角褐指藻的生物技术应用价值提供支撑。