Comparison of a PreQ1 Riboswitch Aptamer in Metabolite-bound and Free States with Implications for Gene Regulation
Comparison of a PreQ1 Riboswitch Aptamer in Metabolite-bound and Free States with Implications for Gene Regulation
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DOI：
10.1074/jbc.m111.230375
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发表时间：
2011-07-15
影响因子：
4.8
通讯作者：
Wedekind, Joseph E.
中科院分区：
文献类型：
--
作者：
Jenkins, Jermaine L.;Krucinska, Jolanta;Wedekind, Joseph E.
核糖开关是一种RNA调控元件，通过高亲和力适配子结构域识别小分子配体来调控基因表达。分子识别可以通过控制转录或翻译所需的mRNA信号的可及性来导致基因表达状态的活跃或减弱。研究的关键领域集中在适配子如何获得其效应器的特异性，适配子在遇到其配体之前折叠的程度，以及配体结合如何改变表达信号的可及性。在这里，我们提出了前Q(1)结合和自由态的前Q(1)核糖开关的晶体结构。尽管preQ(1)的识别模式与对preQ(0)的识别模式相似，但表面等离子体共振显示，preQ(1)的表观K-D为2.1+/-0.3 nm，而preQ(0)的K-D为35.1+/-6.1 nm。这种差异可以通过适体的preQ(1)甲胺和碱基G5之间的相互作用来解释。为了探索在没有代谢物的情况下的构象状态，确定了自由态适配子结构。A14从配基口袋的顶端转移到preQ(1)结合部位，导致对代谢物的“封闭”访问，同时增加核糖体结合部位的暴露。溶液散射数据表明自由态适配子是致密的，但封闭的自由态晶体结构不足以描述溶液散射数据。这些观察结果与同一类转录前Q(1)核糖开关不同，后者表现出严格的配体依赖的折叠。文中还讨论了基因调控的意义。
Riboswitches are RNA regulatory elements that govern gene expression by recognition of small molecule ligands via a high affinity aptamer domain. Molecular recognition can lead to active or attenuated gene expression states by controlling accessibility to mRNA signals necessary for transcription or translation. Key areas of inquiry focus on how an aptamer attains specificity for its effector, the extent to which the aptamer folds prior to encountering its ligand, and how ligand binding alters expression signal accessibility. Here we present crystal structures of the preQ(1) riboswitch from Thermoanaerobacter tengcongensis in the preQ(1)-bound and free states. Although the mode of preQ(1) recognition is similar to that observed for preQ(0), surface plasmon resonance revealed an apparent K-D of 2.1 +/- 0.3 nM for preQ(1) but a value of 35.1 +/- 6.1 nM for preQ(0). This difference can be accounted for by interactions between the preQ(1) methylamine and base G5 of the aptamer. To explore conformational states in the absence of metabolite, the free-state aptamer structure was determined. A14 from the ceiling of the ligand pocket shifts into the preQ(1)-binding site, resulting in "closed" access to the metabolite while simultaneously increasing exposure of the ribosome-binding site. Solution scattering data suggest that the free-state aptamer is compact, but the "closed" free-state crystal structure is inadequate to describe the solution scattering data. These observations are distinct from transcriptional preQ(1) riboswitches of the same class that exhibit strictly ligand-dependent folding. Implications for gene regulation are discussed.