Pokhilko Alexandra
Institute of Molecular, Cell and Systems Biology, University of Glasgow, Glasgow, Scotland, UK.
BMC Syst Biol. 2017 Nov 21;11(1):106. doi: 10.1186/s12918-017-0490-5.
E. coli can be used as bacterial cell factories for production of biofuels and other useful compounds. The efficient production of the desired products requires careful monitoring of growth conditions and the optimization of metabolic fluxes. To avoid nutrient depletion and maximize product yields we suggest using a natural mechanism for sensing nutrient limitation, related to biosynthesis of an intracellular messenger - guanosine tetraphosphate (ppGpp).
We propose a design for a biosensor, which monitors changes in the intracellular concentration of ppGpp by coupling it to a fluorescent output. We used mathematical modelling to analyse the intracellular dynamics of ppGpp, its fluorescent reporter, and cell growth in normal and fatty acid-producing E. coli lines. The model integrates existing mechanisms of ppGpp regulation and predicts the biosensor response to changes in nutrient state. In particular, the model predicts that excessive stimulation of fatty acid production depletes fatty acid intermediates, downregulates growth and increases the levels of ppGpp-related fluorescence.
Our analysis demonstrates that the ppGpp sensor can be used for early detection of nutrient limitation during cell growth and for testing productivity of engineered lines.
大肠杆菌可作为生产生物燃料和其他有用化合物的细菌细胞工厂。高效生产所需产品需要仔细监测生长条件并优化代谢通量。为避免营养物质耗尽并使产品产量最大化，我们建议使用一种与细胞内信使鸟苷四磷酸（ppGpp）生物合成相关的感知营养限制的天然机制。
我们提出了一种生物传感器的设计方案，该方案通过将细胞内ppGpp浓度的变化与荧光输出相耦合来进行监测。我们使用数学模型分析了ppGpp、其荧光报告基因在正常和产脂肪酸的大肠杆菌系中的细胞内动态以及细胞生长情况。该模型整合了现有的ppGpp调节机制，并预测了生物传感器对营养状态变化的响应。特别是，该模型预测脂肪酸生产的过度刺激会耗尽脂肪酸中间体，下调生长并增加与ppGpp相关的荧光水平。
我们的分析表明，ppGpp传感器可用于细胞生长过程中营养限制的早期检测以及工程菌株生产力的测试。
