Sequence preference in RNA recognition by the nucleoporin Nup153
Sequence preference in RNA recognition by the nucleoporin Nup153
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DOI：
10.1074/jbc.m608477200
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发表时间：
2007-03-23
影响因子：
4.8
通讯作者：
Ullman, Katharine S.
中科院分区：
文献类型：
--
作者：
Ball, Jennifer R.;Dimaano, Christian;Ullman, Katharine S.
脊椎动物核孔蛋白Nup 153含有一个新的RNA结合结构域。以前发现，与结构化RNA（如tRNA、U snRNA和双链RNA）相比，这个150个氨基酸的区域优先与一组mRNA结合。广泛识别mRNA的能力导致Nup 153 RNA结合结构域赋予单链RNA的一般亲和力的结论。在这里，我们探测了Nup 153 RNA识别，以破译这种独特的RNA结合结构域如何区分潜在的靶点。我们首先映射的结合决定簇内的RNA片段相关联的Nup 153 RNA结合结构域相对稳健。接下来，我们设计了合成的RNA寡核苷酸，以系统地描述这个最小RNA片段中对Nup 153 RNA结合结构域结合至关重要的特征，并证明Nup 153的结合偏好并不反映mRNA/单链RNA结合蛋白的一般偏好。我们进一步发现，Nup 153和细胞mRNA之间的关联可以归因于与RNA的特定亚区的相互作用。这些结果表明，Nup 153可以区分mRNA和其他类别的RNA转录本，部分原因是直接识别一个松散的序列基序。这些信息为界面增加了一个新的维度，有助于mRNA输出货物选择和命运的识别。
The vertebrate nuclear pore protein Nup153 contains a novel RNA binding domain. This 150-amino acid region was previously found to bind preferentially to a panel of mRNAs when compared with structured RNAs, such as tRNA, U snRNA, and double-stranded RNA. The ability to broadly recognize mRNA led to the conclusion that the Nup153 RNA binding domain confers a general affinity for single-stranded RNA. Here, we have probed Nup153 RNA recognition to decipher how this unique RNA binding domain discriminates between potential targets. We first mapped the binding determinant within an RNA fragment that associates relatively robustly with the Nup153 RNA binding domain. We next designed synthetic RNA oligonucleotides to systematically delineate the features within this minimal RNA fragment that are key to Nup153 RNA-binding domain binding and demonstrated that the binding preferences of Nup153 do not reflect general preferences of an mRNA/single-stranded RNA-binding protein. We further found that the association between Nup153 and a cellular mRNA can be attributed to an interaction with specific subregions of the RNA. These results indicate that Nup153 can discriminate between mRNA and other classes of RNA transcripts due in part to direct recognition of a loose sequence motif. This information adds a new dimension to the interfaces that can contribute to recognition in mRNA export cargo selection and fate.