Metabolomics Infrastructure Group, Max-Planck Institute of Molecular Plant Physiology, 14476, Potsdam, Germany.
Bioinformatics, Institute of Biochemistry and Biology, University of Potsdam, 14476, Potsdam, Germany.
Sci Rep. 2021 Feb 26;11(1):4787. doi: 10.1038/s41598-021-84114-y.
Ribosome biogenesis is tightly associated to plant metabolism due to the usage of ribosomes in the synthesis of proteins necessary to drive metabolic pathways. Given the central role of ribosome biogenesis in cell physiology, it is important to characterize the impact of different components involved in this process on plant metabolism. Double mutants of the Arabidopsis thaliana cytosolic 60S maturation factors REIL1 and REIL2 do not resume growth after shift to moderate 10 [Formula: see text] chilling conditions. To gain mechanistic insights into the metabolic effects of this ribosome biogenesis defect on metabolism, we developed TC-iReMet2, a constraint-based modelling approach that integrates relative metabolomics and transcriptomics time-course data to predict differential fluxes on a genome-scale level. We employed TC-iReMet2 with metabolomics and transcriptomics data from the Arabidopsis Columbia 0 wild type and the reil1-1 reil2-1 double mutant before and after cold shift. We identified reactions and pathways that are highly altered in a mutant relative to the wild type. These pathways include the Calvin-Benson cycle, photorespiration, gluconeogenesis, and glycolysis. Our findings also indicated differential NAD(P)/NAD(P)H ratios after cold shift. TC-iReMet2 allows for mechanistic hypothesis generation and interpretation of system biology experiments related to metabolic fluxes on a genome-scale level.
核糖体生物发生与植物代谢密切相关，因为核糖体在合成驱动代谢途径所需的蛋白质中发挥作用。鉴于核糖体生物发生在细胞生理学中的核心作用，因此表征参与该过程的不同成分对植物代谢的影响非常重要。拟南芥细胞质 60S 成熟因子 REIL1 和 REIL2 的双突变体在转移到适度的 10°C 冷胁迫条件下不能恢复生长。为了深入了解这种核糖体生物发生缺陷对代谢的代谢影响的机制，我们开发了 TC-iReMet2，这是一种基于约束的建模方法，它整合了相对代谢组学和转录组学时间过程数据，以在基因组水平上预测差异通量。我们使用 TC-iReMet2 对拟南芥哥伦比亚 0 野生型和 reil1-1 reil2-1 双突变体在冷胁迫前后的代谢组学和转录组学数据进行了分析。我们确定了在突变体中相对于野生型高度改变的反应和途径。这些途径包括卡尔文-本森循环、光呼吸、糖异生和糖酵解。我们的研究结果还表明，冷胁迫后 NAD(P)/NAD(P)H 比值存在差异。TC-iReMet2 允许在基因组水平上对与代谢通量相关的系统生物学实验进行机制假设生成和解释。
