Department of Cell Biology, Faculty of Biological Sciences, Complutense University of Madrid, 28040 Madrid, Spain.
Biomolecules. 2023 Apr 28;13(5):765. doi: 10.3390/biom13050765.
Quantification of the concentration of particular cellular metabolites reports on the actual utilization of metabolic pathways in physiological and pathological conditions. Metabolite concentration also constitutes the readout for screening cell factories in metabolic engineering. However, there are no direct approaches that allow for real-time assessment of the levels of intracellular metabolites in single cells. In recent years, the modular architecture of natural bacterial RNA riboswitches has inspired the design of genetically encoded synthetic RNA devices that convert the intracellular concentration of a metabolite into a quantitative fluorescent signal. These so-called RNA-based sensors are composed of a metabolite-binding RNA aptamer as the sensor domain, connected through an actuator segment to a signal-generating reporter domain. However, at present, the variety of available RNA-based sensors for intracellular metabolites is still very limited. Here, we go through natural mechanisms for metabolite sensing and regulation in cells across all kingdoms, focusing on those mediated by riboswitches. We review the design principles underlying currently developed RNA-based sensors and discuss the challenges that hindered the development of novel sensors and recent strategies to address them. We finish by introducing the current and potential applicability of synthetic RNA-based sensors for intracellular metabolites.
特定细胞代谢物浓度的定量分析报告了生理和病理条件下代谢途径的实际利用情况。代谢物浓度也是代谢工程中筛选细胞工厂的读出值。然而，目前还没有直接的方法可以实时评估单个细胞内代谢物的水平。近年来，天然细菌 RNA 核糖开关的模块化结构激发了设计基因编码的合成 RNA 设备的灵感，这些设备将代谢物的细胞内浓度转化为定量荧光信号。这些所谓的基于 RNA 的传感器由代谢物结合的 RNA 适体作为传感器结构域组成，通过一个执行器片段与信号产生的报告器结构域相连。然而，目前，可用于细胞内代谢物的基于 RNA 的传感器的种类仍然非常有限。在这里，我们研究了所有生物界中细胞内代谢物感应和调节的自然机制，重点关注那些由核糖开关介导的机制。我们回顾了目前开发的基于 RNA 的传感器的设计原则，并讨论了阻碍新型传感器发展的挑战以及最近解决这些挑战的策略。最后，我们介绍了合成 RNA 基细胞内代谢物传感器的当前和潜在适用性。
