Microbial acclimation to different temperature conditions can involve broad changes in cell composition and metabolic efficiency. A systems-level view of these metabolic responses in non-mesophilic organisms, however, is currently missing. In this study, thermodynamically-constrained genome-scale models were applied to simulate the metabolic responses of a deep-sea psychrophilic bacterium, Shewanella psychrophila WP2, under suboptimal (4°C), optimal (15°C), and supraoptimal (20°C) growth temperatures. The models were calibrated with experimentally determined growth rates of WP2. Gibbs free energy change of reactions (Δ_rG’), metabolic fluxes, and metabolite concentrations were predicted using random simulations to characterize temperature-dependent changes in the metabolism. The modeling revealed the highest metabolic efficiency at the optimal temperature, and it suggested distinct patterns of ATP production and consumption that could lead to the lower metabolic efficiency under suboptimal or supraoptimal temperatures. The modeling also predicted rearrangement of fluxes through multiple metabolic pathways, including the glycolysis pathway, Entner-Doudoroff pathway, tricarboxylic acid (TCA) cycle, and the electron transport system, and these predictions were corroborated through comparisons to WP2 transcriptomes. Furthermore, predictions of metabolite concentrations revealed the potential conservation of reducing equivalents and ATP in the suboptimal temperature, consistent with experimental observations from other psychrophiles. Taken together, the WP2 models provided mechanistic insights into the metabolism of a psychrophile in response to different temperatures.

中文翻译：

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热力学约束模型的重建和分析揭示了深海细菌对温度扰动的代谢反应

微生物对不同温度条件的适应可能涉及细胞组成和代谢效率的广泛变化。然而，目前缺少非嗜温生物中这些代谢反应的系统级视图。在这项研究中，应用热力学约束的基因组规模模型来模拟深海嗜冷菌Shewanella psychrophila WP2 在次优 (4°C)、最佳 (15°C) 和超优 (20° C) 生长温度。用实验确定的 WP2 生长速率校准模型。反应的吉布斯自由能变化 ( Δ _r G')、代谢通量和代谢物浓度是使用随机模拟预测的，以表征代谢中温度依赖性变化。该模型揭示了在最佳温度下最高的代谢效率，它表明了 ATP 生产和消耗的不同模式，这可能导致在次优或超优温度下代谢效率降低。该模型还预测了通过多种代谢途径的通量重排，包括糖酵解途径、Entner-Doudoroff 途径、三羧酸 (TCA) 循环和电子传递系统，这些预测通过与 WP2 转录组的比较得到证实。此外，代谢物浓度的预测揭示了在次优温度下还原当量和 ATP 的潜在保守性，与其他嗜冷菌的实验观察结果一致。总之，WP2 模型提供了对嗜冷菌响应不同温度的代谢的机制见解。