Crystal structure of a Y-box binding protein 1 (YB-1)-RNA complex reveals key features and residues interacting with RNA
Crystal structure of a Y-box binding protein 1 (YB-1)-RNA complex reveals key features and residues interacting with RNA
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Y-box 结合蛋白 1 (YB-1)-RNA 复合物的晶体结构揭示了与 RNA 相互作用的关键特征和残基
DOI：
10.1074/jbc.ra119.007545
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发表时间：
2019
影响因子：
4.8
通讯作者：
Huang Ying
中科院分区：
文献类型：
--
作者：
Yang Xiaojuan;Zhu Hong;Mu Shirong;Wei Wenjuan;Yuan Xun;Wang Meng;Liu Yanchao;Hui Jingyi;Huang Ying
Y-box结合蛋白1（YB-1）是冷休克结构域（CSD）蛋白家族的成员，并且被认为是几种实体瘤中的致癌因子。通过与RNA结合，YB-1参与基因表达的转录后调节的几个步骤，包括mRNA剪接、稳定性和翻译; microRNA加工;和应激颗粒组装。然而，YB-1介导的RNA调控机制尚不清楚。在此之前，我们使用了通过指数富集的配体系统进化（SELEX）和单个核苷酸分辨率UV交联和免疫沉淀耦合RNA-Seq（iCLIP-Seq）分析，其将YB-1的RNA结合共有序列定义为CA（U/C）C。我们还报道了YB-1通过与初级转录物中的核心基序CAUC结合，在Drosha和Dicer步骤中调节aCD 44可变外显子的选择性剪接和miR-29 b-2的生物合成。为了阐明YB-1-RNA相互作用的分子基础，我们报道了YB-1 CSD与不同RNA寡核苷酸复合物的高分辨率晶体结构，分辨率为1.7 nm。结构分析表明，CSD与RNA的相互作用主要是通过4个高度保守的芳香残基组成的π-π堆积作用实现的。有趣的是，YB-1 CSD在溶液中形成同源二聚体，并且我们观察到二聚体界面处的两个残基Tyr-99和Asp-105对于YB-1 CSD二聚化是重要的。用Ala取代这两个残基降低了CSD的RNA结合活性，并消除了YB-1靶标的剪接激活。这里以原子分辨率呈现的YB-1 CSD-RNA结构提供了对由含CSD蛋白质调控的基因表达的机制见解。
The Y-box binding protein 1 (YB-1) is a member of the cold shock domain (CSD) protein family and is recognized as an oncogenic factor in several solid tumors. By binding to RNA, YB-1 participates in several steps of posttranscriptional regulation of gene expression, including mRNA splicing, stability, and translation; microRNA processing; and stress granule assembly. However, the mechanisms in YB-1–mediated regulation of RNAs are unclear. Previously, we used both systematic evolution of ligands by exponential enrichment (SELEX) and individual-nucleotide resolution UV cross-linking and immunoprecipitation coupled RNA-Seq (iCLIP-Seq) analyses, which defined the RNA-binding consensus sequence of YB-1 as CA(U/C)C. We also reported that through binding to its core motif CAUC in primary transcripts, YB-1 regulates the alternative splicing of aCD44variable exon and the biogenesis of miR-29b-2 during both Drosha and Dicer steps. To elucidate the molecular basis of the YB-1–RNA interactions, we report high-resolution crystal structures of the YB-1 CSD in complex with different RNA oligos at 1.7 Å resolution. The structure revealed that CSD interacts with RNA mainly through π–π stacking interactions assembled by four highly conserved aromatic residues. Interestingly, YB-1 CSD forms a homodimer in solution, and we observed that two residues, Tyr-99 and Asp-105, at the dimer interface are important for YB-1 CSD dimerization. Substituting these two residues with Ala reduced CSD's RNA-binding activity and abrogated the splicing activation of YB-1 targets. The YB-1 CSD–RNA structures presented here at atomic resolution provide mechanistic insights into gene expression regulated by CSD-containing proteins.