Center for Theoretical Biological Physics, Rice University, Houston, TX 77005, USA.
Theoretical Biology and Biophysics Group, Theoretical Division, Los Alamos National Laboratory, Los Alamos, NM 87545, USA.
Nucleic Acids Res. 2019 Apr 8;47(6):3158-3170. doi: 10.1093/nar/gky1311.
Investigations of most riboswitches remain confined to the ligand-binding aptamer domain. However, during the riboswitch mediated transcription regulation process, the aptamer domain and the expression platform compete for a shared strand. If the expression platform dominates, an anti-terminator helix is formed, and the transcription process is active (ON state). When the aptamer dominates, transcription is terminated (OFF state). Here, we use an expression platform switching experimental assay and structure-based electrostatic simulations to investigate this ON-OFF transition of the full length SAM-I riboswitch and its magnesium concentration dependence. Interestingly, we find the ratio of the OFF population to the ON population to vary non-monotonically as magnesium concentration increases. Upon addition of magnesium, the aptamer domain pre-organizes, populating the OFF state, but only up to an intermediate magnesium concentration level. Higher magnesium concentration preferentially stabilizes the anti-terminator helix, populating the ON state, relatively destabilizing the OFF state. Magnesium mediated aptamer-expression platform domain closure explains this relative destabilization of the OFF state at higher magnesium concentration. Our study reveals the functional potential of magnesium in controlling transcription of its downstream genes and underscores the importance of a narrow concentration regime near the physiological magnesium concentration ranges, striking a balance between the OFF and ON states in bacterial gene regulation.
大多数核糖开关的研究仍局限于配体结合的适体结构域。然而，在核糖开关介导的转录调控过程中，适体结构域和表达平台争夺共享链。如果表达平台占主导地位，就会形成反终止子螺旋，转录过程是活跃的（ON 状态）。当适体占主导地位时，转录被终止（OFF 状态）。在这里，我们使用表达平台转换实验测定和基于结构的静电模拟来研究全长 SAM-I 核糖开关及其镁浓度依赖性的这种 ON-OFF 转变。有趣的是，我们发现随着镁浓度的增加，OFF 群体与 ON 群体的比例呈非单调变化。加入镁后，适体结构域预先组织，占据 OFF 状态，但仅在中间镁浓度水平。较高的镁浓度优先稳定反终止子螺旋，使 ON 状态占据主导地位，相对地使 OFF 状态不稳定。镁介导的适体-表达平台结构域关闭解释了在较高镁浓度下 OFF 状态的相对不稳定。我们的研究揭示了镁在控制其下游基因转录中的功能潜力，并强调了在生理镁浓度范围内接近窄浓度范围的重要性，在细菌基因调控中在 OFF 和 ON 状态之间取得平衡。
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