Structural and Computational Biology Unit, EMBL Heidelberg, Meyerhofstraße 1, 69117 Heidelberg, Germany; Collaboration for Joint PhD Degree between EMBL and Heidelberg University, Faculty of Biosciences, Heidelberg, Germany.
Structural and Computational Biology Unit, EMBL Heidelberg, Meyerhofstraße 1, 69117 Heidelberg, Germany.
Cell Rep. 2020 Jul 21;32(3):107930. doi: 10.1016/j.celrep.2020.107930.
RNA-binding proteins (RBPs) commonly feature multiple RNA-binding domains (RBDs), which provide these proteins with a modular architecture. Accumulating evidence supports that RBP architectural modularity and adaptability define the specificity of their interactions with RNA. However, how multiple RBDs recognize their cognate single-stranded RNA (ssRNA) sequences in concert remains poorly understood. Here, we use Upstream of N-Ras (Unr) as a model system to address this question. Although reported to contain five ssRNA-binding cold-shock domains (CSDs), we demonstrate that Unr includes an additional four CSDs that do not bind RNA (pseudo-RBDs) but are involved in mediating RNA tertiary structure specificity by reducing the conformational heterogeneity of Unr. Disrupting the interactions between canonical and non-canonical CSDs impacts RNA binding, Unr-mediated translation regulation, and the Unr-dependent RNA interactome. Taken together, our studies reveal a new paradigm in protein-RNA recognition, where interactions between RBDs and pseudo-RBDs select RNA tertiary structures, influence RNP assembly, and define target specificity.
RNA 结合蛋白 (RBPs) 通常具有多个 RNA 结合结构域 (RBDs)，为这些蛋白提供了模块化的结构。越来越多的证据支持 RBP 结构的模块化和适应性决定了它们与 RNA 相互作用的特异性。然而，多个 RBD 如何协同识别其同源的单链 RNA (ssRNA) 序列仍知之甚少。在这里，我们使用 Upstream of N-Ras (Unr) 作为模型系统来解决这个问题。尽管报道称含有五个 ssRNA 结合冷休克结构域 (CSDs)，但我们证明 Unr 还包含另外四个不结合 RNA 的 CSD（假 RBDs），但通过降低 Unr 的构象异质性来参与调节 RNA 三级结构特异性。破坏规范和非规范 CSD 之间的相互作用会影响 RNA 结合、Unr 介导的翻译调控以及 Unr 依赖的 RNA 相互作用组。总之，我们的研究揭示了蛋白质-RNA 识别的一个新范例，其中 RBDs 和假 RBDs 之间的相互作用选择 RNA 三级结构、影响 RNP 组装并定义靶标特异性。
