Conformational heterogeneity of the SAM-I riboswitch transcriptional ON state: a chaperone-like role for S-adenosyl methionine.
Conformational heterogeneity of the SAM-I riboswitch transcriptional ON state: a chaperone-like role for S-adenosyl methionine.
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DOI：
10.1016/j.jmb.2012.02.019
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发表时间：
2012-05-18
影响因子：
5.6
通讯作者：
Aboul-Ela F
中科院分区：
文献类型：
--
作者：
Huang W;Kim J;Jha S;Aboul-Ela F
核糖开关是设计新型抗生素和工程化的便携式基因调控元件的有前途的目标。有证据表明，核糖开关特性的可变性允许通过目前尚不清楚的机制来调节参与生物合成途径不同阶段的基因的表达。在这里，我们探索的机制，调整SAM-I核糖开关折叠。大多数SAM-I核糖开关通过感应同源配体-S-腺苷甲硫氨酸（SAM）在转录水平上起作用。SAM-I核糖开关协调半胱氨酸、蛋氨酸和SAM等的生物合成途径。我们使用碱基对概率预测来研究几个SAM-I核糖开关序列的二级结构折叠景观。我们预测不同的SAM-I核糖开关序列的不同折叠行为。我们确定了几个“诱饵”碱基配对相互作用，涉及5'核糖开关残基，可以与P1螺旋的形成竞争，配体结合的“转录关闭”状态的组成部分，在SAM的情况下。我们假设，通过SAM接触这些相互作用的阻断有助于在配体存在下稳定OFF状态。我们还使用具有不同3'截短点的构建体实验性地探测SAM-I核糖开关RNA的折叠模式。通过荧光、对碱催化裂解的敏感性、核磁共振和间接通过SAM结合监测折叠。我们确定了关键的决策窗口，SAM可以影响折叠途径向关闭状态。诱饵构象的存在和不同的敏感性SAM在不同的转录本长度是至关重要的SAM-1核糖开关，以调节基因表达的背景下，全球细胞代谢。
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 SAM-I riboswitch folding. Most SAM-I riboswitches function at the transcriptional level by sensing the cognate ligand— S-adenosyl methionine (SAM). SAM-I riboswitches orchestrate the biosynthetic pathways of cysteine, methionine and SAM, etc. 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 toward the OFF state. The presence of decoy conformations and differential sensitivities to SAM at different transcript lengths are crucial for SAM-I riboswitches to modulate gene expression in the context of global cellular metabolism.