Institute of Molecular Biology and Biotechnology, Faculty of Biology, Adam Mickiewicz University, Uniwersytetu Poznańskiego 6, 61-614 Poznań, Poland; T.C. Jenkins Department of Biophysics, Johns Hopkins University, Baltimore, MD 21218, USA.
Institute of Molecular Biology and Biotechnology, Faculty of Biology, Adam Mickiewicz University, Uniwersytetu Poznańskiego 6, 61-614 Poznań, Poland; Institute of Bioorganic Chemistry, Polish Academy of Sciences, Noskowskiego 12/14, 61-704 Poznań, Poland. Electronic address: https://twitter.com/SobanskaD.
J Mol Biol. 2021 Nov 19;433(23):167291. doi: 10.1016/j.jmb.2021.167291. Epub 2021 Oct 5.
Bacterial small RNAs (sRNAs) in association with the chaperone protein Hfq regulate the expression of many target mRNAs. Since sRNAs' action is crucial to engendering a response to changing environmental conditions, their activity needs to be regulated. One such mechanism occurs at the post-transcriptional level and involves sponge RNAs, which sequester sRNAs affecting their regulatory output. Both types of RNAs were identified on Hfq, but it is not known how Hfq interacts with RNA sponges and stimulates their base-pairing with sRNAs. Here, we used biochemical methods to demonstrate that sponge RNAs resemble sRNAs by their structure and their modes of Hfq binding. Hfq facilitates the annealing of AgvB and 3'ETS sponge RNAs to targeted sRNAs: GcvB and RybB, respectively, and each surface of the protein plays a particular role in the process. Moreover, we found that the efficiency of sponge RNA interactions with sRNAs can be improved; therefore, we propose that natural RNA sponges might not sequester sRNAs optimally.
细菌小 RNA（sRNA）与伴侣蛋白 Hfq 结合，调节许多靶 mRNA 的表达。由于 sRNA 的作用对于产生对环境变化的反应至关重要，因此需要对其活性进行调节。这种机制之一发生在转录后水平，涉及海绵 RNA，它可以隔离 sRNA，从而影响其调节输出。这两种 RNA 都在 Hfq 上被鉴定出来，但目前尚不清楚 Hfq 如何与 RNA 海绵相互作用并刺激它们与 sRNA 形成碱基配对。在这里，我们使用生化方法证明海绵 RNA 在结构和 Hfq 结合方式上与 sRNA 相似。Hfq 促进 AgvB 和 3'ETS 海绵 RNA 与靶向 sRNA：GcvB 和 RybB 分别退火，蛋白质的每个表面在该过程中都发挥特定作用。此外，我们发现海绵 RNA 与 sRNA 的相互作用效率可以提高；因此，我们提出天然 RNA 海绵可能不能最佳地隔离 sRNA。
