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首页> 外文期刊>Journal of Molecular Biology >Conformational heterogeneity of the SAM-I riboswitch transcriptional on state: A chaperone-like role for S-adenosyl methionine
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Conformational heterogeneity of the SAM-I riboswitch transcriptional on state: A chaperone-like role for S-adenosyl methionine

机译：SAM-1核糖开关转录的构象异质性：S-腺苷蛋氨酸的伴侣样作用

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摘要

Riboswitches are promising targets for the design of novel antibiotics and engineering of portable genetic regulatory elements. There is evidence that variability in riboswitch properties allows tuning of expression for genes involved in different stages of biosynthetic pathways by mechanisms that are not currently understood. Here, we explore the mechanism for tuning of S-adenosyl methionine (SAM)-I riboswitch folding. Most SAM-I riboswitches function at the transcriptional level by sensing the cognate ligand SAM. SAM-I riboswitches orchestrate the biosynthetic pathways of cysteine, methionine, SAM, and so forth. We use base-pair probability predictions to examine the secondary-structure folding landscape of several SAM-I riboswitch sequences. We predict different folding behaviors for different SAM-I riboswitch sequences. We identify several "decoy" base-pairing interactions involving 5′ riboswitch residues that can compete with the formation of a P1 helix, a component of the ligand-bound "transcription OFF" state, in the absence of SAM. We hypothesize that blockage of these interactions through SAM contacts contributes to stabilization of the OFF state in the presence of ligand. We also probe folding patterns for a SAM-I riboswitch RNA using constructs with different 3′ truncation points experimentally. Folding was monitored through fluorescence, susceptibility to base-catalyzed cleavage, nuclear magnetic resonance, and indirectly through SAM binding. We identify key decision windows at which SAM can affect the folding pathway towards the OFF state. The presence of decoy conformations and differential sensitivities to SAM at different transcript lengths is crucial for SAM-I riboswitches to modulate gene expression in the context of global cellular metabolism.
机译：Riboswitches是设计新型抗生素和便携式遗传调节元件的设计的目标。有证据表明，核糖场所性能的可变性允许通过目前未理解的机制调整参与生物合成途径的不同阶段的基因的表达。在此，我们探讨调整S-腺苷蛋氨酸（SAM）-I核糖开关折叠的机制。大多数SAM-1通过感测同源配体SAM通过转录水平函数。 Sam-i riboswitches编排半胱氨酸，蛋氨酸，山姆等的生物合成途径。我们使用基对概率预测来检查几个SAM-1核序列序列的二级结构折叠景观。我们预测不同的SAM-I Riboswitch序列的不同折叠行为。我们鉴定了涉及5'核糖场所残留物的几个“诱饵”碱基配对相互作用，其能够与P1螺旋的形成竞争，在没有SAM的情况下，可以竞争P1螺旋的组分。我们假设通过SAM触点阻塞这些相互作用有助于在配体存在下稳定OFF状态。我们还通过实验使用不同的3'截断点的构造探测SAM-I Riboswitch RNA的折叠模式。通过荧光，对碱催化的裂解，核磁共振，间接通过SAM结合间接监测折叠。我们识别SAM可以影响折叠通路朝向关闭状态的关键决策窗口。在不同的转录长度下对SAM的诱饵构象和差异敏感性对SAM-1核糖开关在全局细胞代谢的背景下调节基因表达至关重要。

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