Department of Food Science & Engineering, Ewha Womans University, 11-1 Daehyun-dong, Seodaemun-gu, Seoul 120-750, Korea.
Microb Cell Fact. 2014 Apr 28;13:61. doi: 10.1186/1475-2859-13-61.
Thermus thermophilus, an extremely thermophilic bacterium, has been widely recognized as a model organism for studying how microbes can survive and adapt under high temperature environment. However, the thermotolerant mechanisms and cellular metabolism still remains mostly unravelled. Thus, it is highly required to consider systems biological approaches where T. thermophilus metabolic network model can be employed together with high throughput experimental data for elucidating its physiological characteristics under such harsh conditions.
We reconstructed a genome-scale metabolic model of T. thermophilus, iTT548, the first ever large-scale network of a thermophilic bacterium, accounting for 548 unique genes, 796 reactions and 635 unique metabolites. Our initial comparative analysis of the model with Escherichia coli has revealed several distinctive metabolic reactions, mainly in amino acid metabolism and carotenoid biosynthesis, producing relevant compounds to retain the cellular membrane for withstanding high temperature. Constraints-based flux analysis was, then, applied to simulate the metabolic state in glucose minimal and amino acid rich media. Remarkably, resulting growth predictions were highly consistent with the experimental observations. The subsequent comparative flux analysis under different environmental conditions highlighted that the cells consumed branched chain amino acids preferably and utilized them directly in the relevant anabolic pathways for the fatty acid synthesis. Finally, gene essentiality study was also conducted via single gene deletion analysis, to identify the conditional essential genes in glucose minimal and complex media.
The reconstructed genome-scale metabolic model elucidates the phenotypes of T. thermophilus, thus allowing us to gain valuable insights into its cellular metabolism through in silico simulations. The information obtained from such analysis would not only shed light on the understanding of physiology of thermophiles but also helps us to devise metabolic engineering strategies to develop T. thermophilus as a thermostable microbial cell factory.
嗜热栖热菌是一种极端嗜热的细菌，已被广泛认为是研究微生物如何在高温环境中生存和适应的模式生物。然而，其耐热机制和细胞代谢仍大多未被揭示。因此，非常需要考虑系统生物学方法，其中可以使用嗜热栖热菌代谢网络模型并结合高通量实验数据来阐明其在这种苛刻条件下的生理特征。
我们构建了嗜热栖热菌 iTT548 的基因组规模代谢模型，这是第一个大规模的嗜热菌网络，包含 548 个独特基因、796 个反应和 635 个独特代谢物。我们对该模型与大肠杆菌的初步比较分析揭示了几种独特的代谢反应，主要在氨基酸代谢和类胡萝卜素生物合成中，产生相关化合物以保持细胞膜耐受高温。然后，基于约束的通量分析被应用于模拟葡萄糖最小和氨基酸丰富培养基中的代谢状态。值得注意的是，由此产生的生长预测与实验观察高度一致。随后在不同环境条件下的比较通量分析强调，细胞优先消耗支链氨基酸，并直接将其用于脂肪酸合成的相关合成途径中。最后，还通过单基因缺失分析进行了基因必需性研究，以鉴定葡萄糖最小和复杂培养基中的条件必需基因。
重建的基因组规模代谢模型阐明了嗜热栖热菌的表型，从而使我们能够通过计算机模拟深入了解其细胞代谢。从这种分析中获得的信息不仅有助于理解嗜热菌的生理学，还有助于我们设计代谢工程策略，将嗜热栖热菌开发为耐热微生物细胞工厂。
