Lavoie Michel, Saint-Béat Blanche, Strauss Jan, Guérin Sébastien, Allard Antoine, V Hardy Simon, Falciatore Angela, Lavaud Johann
Unité Mixte Internationale 3376 Takuvik, CNRS-ULaval, Département de Biologie and Québec-Océan, Université Laval, Québec, QC G1V 0A6, Canada.
Department of Biology, University of Hamburg, D-22607 Hamburg, Germany.
Biology (Basel). 2020 Feb 17;9(2):30. doi: 10.3390/biology9020030.
Diatoms are major primary producers in polar environments where they can actively grow under extremely variable conditions. Integrative modeling using a genome-scale model (GSM) is a powerful approach to decipher the complex interactions between components of diatom metabolism and can provide insights into metabolic mechanisms underlying their evolutionary success in polar ecosystems. We developed the first GSM for a polar diatom, , which enabled us to study its metabolic robustness using sensitivity analysis. We find that the predicted growth rate was robust to changes in all model parameters (i.e., cell biochemical composition) except the carbon uptake rate. Constraints on total cellular carbon buffer the effect of changes in the input parameters on reaction fluxes and growth rate. We also show that single reaction deletion of 20% to 32% of active (nonzero flux) reactions and single gene deletion of 44% to 55% of genes associated with active reactions affected the growth rate, as well as the production fluxes of total protein, lipid, carbohydrate, DNA, RNA, and pigments by less than 1%, which was due to the activation of compensatory reactions (e.g., analogous enzymes and alternative pathways) with more highly connected metabolites involved in the reactions that were robust to deletion. Interestingly, including highly divergent alleles unique for increased its metabolic robustness to cellular perturbations even more. Overall, our results underscore the high robustness of metabolism in , a feature that likely helps to maintain cell homeostasis under polar conditions.
硅藻是极地环境中的主要初级生产者，它们能够在极端多变的条件下积极生长。使用基因组规模模型（GSM）进行综合建模是一种强大的方法，可用于解读硅藻代谢各组分之间的复杂相互作用，并能深入了解其在极地生态系统中进化成功所依据的代谢机制。我们为一种极地硅藻开发了首个GSM，这使我们能够通过敏感性分析来研究其代谢稳健性。我们发现，除了碳吸收速率外，预测的生长速率对所有模型参数（即细胞生化组成）的变化都具有稳健性。细胞总碳的限制缓冲了输入参数变化对反应通量和生长速率的影响。我们还表明，20%至32%的活跃（非零通量）反应的单反应删除以及与活跃反应相关的44%至55%的基因的单基因删除，对生长速率以及总蛋白质、脂质、碳水化合物、DNA、RNA和色素的生产通量的影响小于1%，这是由于涉及到对删除具有稳健性的反应中连接性更高的代谢物的补偿反应（如类似酶和替代途径）的激活。有趣的是，纳入该硅藻特有的高度分化等位基因进一步增强了其对细胞扰动的代谢稳健性。总体而言，我们的结果强调了该硅藻代谢的高度稳健性，这一特性可能有助于在极地条件下维持细胞内稳态。
