单分子 FRET 揭示全长 SAM-I 核糖开关的能量景观。

Single-molecule FRET reveals the energy landscape of the full-length SAM-I riboswitch.

机构信息

Institute of Applied Physics, Karlsruhe Institute of Technology, Karlsruhe, Germany.

Heidelberg Karlsruhe Research Partnership (HEiKA), Karlsruhe Institute of Technology, Eggenstein-Leopoldshafen, Germany.

出版信息

Nat Chem Biol. 2017 Nov;13(11):1172-1178. doi: 10.1038/nchembio.2476. Epub 2017 Sep 18.

Abstract

S-adenosyl-L-methionine (SAM) ligand binding induces major structural changes in SAM-I riboswitches, through which gene expression is regulated via transcription termination. Little is known about the conformations and motions governing the function of the full-length Bacillus subtilis yitJ SAM-I riboswitch. Therefore, we have explored its conformational energy landscape as a function of Mg and SAM ligand concentrations using single-molecule Förster resonance energy transfer (smFRET) microscopy and hidden Markov modeling analysis. We resolved four conformational states both in the presence and the absence of SAM and determined their Mg-dependent fractional populations and conformational dynamics, including state lifetimes, interconversion rate coefficients and equilibration timescales. Riboswitches with terminator and antiterminator folds coexist, and SAM binding only gradually shifts the populations toward terminator states. We observed a pronounced acceleration of conformational transitions upon SAM binding, which may be crucial for off-switching during the brief decision window before expression of the downstream gene.

摘要

S-腺苷甲硫氨酸(SAM)配体结合诱导 SAM-I 核糖开关发生主要结构变化,通过这种变化,基因表达通过转录终止进行调节。关于全长枯草芽孢杆菌 yitJ SAM-I 核糖开关的构象和运动如何控制其功能,我们知之甚少。因此,我们使用单分子Förster 共振能量转移(smFRET)显微镜和隐马尔可夫模型分析,研究了其构象能谱作为 Mg 和 SAM 配体浓度的函数。我们在存在和不存在 SAM 的情况下解析了四个构象状态,并确定了它们的 Mg 依赖性分数种群和构象动力学,包括状态寿命、互变率系数和平衡时间尺度。终止子和反终止子构象的核糖开关共存,并且 SAM 结合仅逐渐将种群转移到终止子状态。我们观察到 SAM 结合后构象转变明显加速,这对于下游基因表达前短暂的决策窗口期间的关闭开关可能至关重要。

文献AI研究员

20分钟写一篇综述,助力文献阅读效率提升50倍

立即体验

用中文搜PubMed

大模型驱动的PubMed中文搜索引擎

马上搜索