Töpfer Nadine, Seaver Samuel M D, Aharoni Asaph
Faculty of Biochemistry, Department of Plant and Environmental Sciences, Weizmann Institute of Science, Rehovot, Israel.
Mathematics and Computer Science Division, Argonne National Laboratory, Argonne, IL, USA.
Methods Mol Biol. 2018;1778:297-310. doi: 10.1007/978-1-4939-7819-9_21.
In the last decade, plant genome-scale modeling has developed rapidly and modeling efforts have advanced from representing metabolic behavior of plant heterotrophic cell suspensions to studying the complex interplay of cell types, tissues, and organs. A crucial driving force for such developments is the availability and integration of "omics" data (e.g., transcriptomics, proteomics, and metabolomics) which enable the reconstruction, extraction, and application of context-specific metabolic networks. In this chapter, we demonstrate a workflow to integrate gas chromatography coupled to mass spectrometry (GC-MS)-based metabolomics data of tomato fruit pericarp (flesh) tissue, at five developmental stages, with a genome-scale reconstruction of tomato metabolism. This method allows for the extraction of context-specific networks reflecting changing activities of metabolic pathways throughout fruit development and maturation.
在过去十年中，植物基因组规模建模发展迅速，建模工作已从描述植物异养细胞悬浮液的代谢行为推进到研究细胞类型、组织和器官之间的复杂相互作用。此类发展的一个关键驱动力是“组学”数据（如转录组学、蛋白质组学和代谢组学）的可用性和整合，这些数据能够重建、提取和应用特定环境下的代谢网络。在本章中，我们展示了一种工作流程，将五个发育阶段的番茄果实果皮（果肉）组织基于气相色谱-质谱联用（GC-MS）的代谢组学数据与番茄代谢的基因组规模重建相结合。该方法能够提取反映果实发育和成熟过程中代谢途径活性变化的特定环境网络。
