Metabolites homeostasis and gene regulation

铁是几乎所有生物体最重要的离子金属之一。Fe是许多酶的辅因子或结构组分，这些酶参与代谢的关键步骤，如呼吸，TCA循环，RNA修饰，DNA合成和基因调控。在低铁条件下生长期间，细菌在其环境中分泌称为铁载体（肠杆菌素）的分子，这使得铁在运输到细胞内之前溶解。几十年来，大肠杆菌铁载体的合成被认为是在转录水平上由铁响应转录抑制子Fur完全调控的。然而，在我们的研究过程中，我们观察到小RNA RyhB对铁载体的正常产生至关重要。首先，RyhB直接抑制cysE的翻译，cysE编码丝氨酸乙酰转移酶，其使用丝氨酸作为半胱氨酸生物合成的底物。通过RyhB减少CysE活性允许丝氨酸用作肠杆菌素合成的结构单元。第二，我们的数据表明，翻译机器成为缺乏时，细胞内Fe稳态丢失。这些惊人的结果强调了一个事实，即尽管经过几十年的深入研究，我们仍然不了解铁的许多关键生理作用。在这个提议中，我们描述了我们将如何研究这些铁依赖的调节机制，如翻译效率和tRNA修饰。此外，作为我们对小RNA和代谢物工作的一般延伸，我们将通过小RNA和核糖开关（最近发现的位于某些mRNA中的RNA结构）探索代谢物稳态的机制。由于小RNA和核糖开关共享它们的一些基本功能，我们希望一起研究这些新机制。因此，我的建议探讨了各种RNA结构和代谢的明显整合背后的机制，以调节细胞内稳态。

Iron (Fe) is one of the most important ion metals for nearly all organisms. Fe is a cofactor or structural component of numerous enzymes that participate in key steps of the metabolism such as respiration, TCA cycle, RNA modification, DNA synthesis, and gene regulation. During growth under low-Fe conditions, bacteria secrete in their environment molecules called siderophores (enterobactin), which makes the Fe soluble before it is transported inside the cell. For decades, the synthesis of siderophores by Escherichia coli was considered to be fully regulated at the transcriptional level by the Fe-responsive transcriptional repressor Fur. However, during the course of our study, we observed that the small RNA RyhB was essential for normal production of siderophores. First, RyhB directly represses the translation of cysE, which encodes a serine acetyltransferase that uses serine as a substrate for cysteine biosynthesis. Reduction of CysE activity by RyhB allows serine to be used as building blocks for enterobactin synthesis. Second, our data indicate that the translational machinery becomes deficient when intracellular Fe homeostasis is lost. These striking results underline the fact that, despite several decades of intensive studies, we still do not understand many key physiological roles of Fe. In this proposal, we describe how we will investigate these Fe-dependent mechanisms of regulation, such as translation efficiency and tRNA modifications. Moreover, as a general extension of our work with small RNAs and metabolites, we will explore the mechanism of metabolite homeostasis through small RNAs and riboswitches, a recently discovered RNA structure located in certain mRNAs. Because small RNAs and riboswitches share some of their fundamental functions, we want to investigate these novel mechanisms together. Hence, my proposal explores the mechanisms behind the apparent integration of various RNA structures and metabolism to regulate intracellular homeostasis.