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首页> 外文期刊>Journal of Molecular Biology >Nucleotides adjacent to the ligand-binding pocket are linked to activity tuning in the purine riboswitch
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Nucleotides adjacent to the ligand-binding pocket are linked to activity tuning in the purine riboswitch

机译：邻近配体结合口袋的核苷酸与嘌呤核糖开关中的活性调节相关

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摘要

Direct sensing of intracellular metabolite concentrations by riboswitch RNAs provides an economical and rapid means to maintain metabolic homeostasis. Since many organisms employ the same class of riboswitch to control different genes or transcription units, it is likely that functional variation exists in riboswitches such that activity is tuned to meet cellular needs. Using a bioinformatic approach, we have identified a region of the purine riboswitch aptamer domain that displays conservation patterns linked to riboswitch activity. Aptamer domain compositions within this region can be divided into nine classes that display a spectrum of activities. Naturally occurring compositions in this region favor rapid association rate constants and slow dissociation rate constants for ligand binding. Using X-ray crystallography and chemical probing, we demonstrate that both the free and bound states are influenced by the composition of this region and that modest sequence alterations have a dramatic impact on activity. The introduction of non-natural compositions result in the inability to regulate gene expression in vivo, suggesting that aptamer domain activity is highly plastic and thus readily tunable to meet cellular needs.
机译：核糖开关RNA直接感测细胞内代谢物的浓度提供了一种经济，快速的方法来维持代谢稳态。由于许多生物体使用同一类核糖开关来控制不同的基因或转录单位，因此核糖开关中可能存在功能变异，因此可以调节其活性以满足细胞的需求。使用生物信息学方法，我们已经确定了嘌呤核糖开关适体结构域的区域，该区域显示了与核糖开关活性相关的保守模式。该区域内的适体结构域组成可分为显示活性谱的九类。该区域中天然存在的组合物有利于配体结合的快速缔合速率常数和缓慢的解离速率常数。使用X射线晶体学和化学探测，我们证明了自由状态和结合状态均受该区域组成的影响，适度的序列变化对活性产生了显着影响。非天然组合物的引入导致无法在体内调节基因表达，这表明适体结构域活性是高度可塑性的，因此易于调节以满足细胞需求。

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