In bacteria, small non-coding RNAs (sRNAs) could function in gene regulations under variable stress responses. DsrA is an ∼90-nucleotide Hfq-dependent sRNA found in Escherichia coli. It regulates the translation and degradation of multiple mRNAs, such as rpoS, hns, mreB and rbsD mRNAs. However, its functional structure and particularly how it regulates multiple mRNAs remain obscure. Using NMR, we investigated the solution structures of the full-length and isolated stem–loops of DsrA. We first solved the NMR structure of the first stem–loop (SL1), and further studied the melting process of the SL1 induced by the base-pairing with the rpoS mRNA and the A-form duplex formation of the DsrA/rpoS complex. The secondary structure of the second stem–loop (SL2) was also determined, which contains a lower stem and an upper stem with distinctive stability. Interestingly, two conformational states of SL2 in dynamic equilibrium were observed in our NMR spectra, suggesting that the conformational selection may occur during the base-pairing between DsrA and mRNAs. In summary, our study suggests that the conformational plasticity of DsrA may represent a special mechanism sRNA employed to deal with its multiple regulatory targets of mRNA.

中文翻译：

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DsrA sRNA对适应多靶标调控的重要构象可塑性

在细菌中，小的非编码RNA（sRNA）可以在可变胁迫反应下在基因调控中发挥作用。DsrA是在大肠杆菌中发现的约90个核苷酸的Hfq依赖性sRNA 。它调节多种mRNA的翻译和降解，例如rpoS，hns，mreB和rbsD mRNA。然而，其功能结构，尤其是其如何调节多种mRNA仍然不清楚。使用NMR，我们研究了DsrA全长和孤立茎环的溶液结构。我们首先解决了第一个茎环（SL1）的NMR结构，并进一步研究了与rpoS mRNA碱基配对和DsrA / rpoS的A型双链体形成诱导的SL1的解链过程复杂的。还确定了第二茎环（SL2）的二级结构，该结构包含下部茎和上部茎，具有独特的稳定性。有趣的是，在我们的NMR光谱中观察到了SL2在动态平衡中的两个构象状态，这表明构象选择可能发生在DsrA与mRNA之间的碱基配对过程中。总而言之，我们的研究表明，DsrA的构象可塑性可能代表了一种特殊的sRNA机制，用于处理其多个mRNA调控靶标。