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 Mg²⁺ 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 Mg²⁺-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.

S-腺苷-L-甲硫氨酸（SAM）配体结合诱导SAM-1核糖开关中的主要结构变化，通过该结构，通过转录终止调节基因表达。关于支配全长枯草芽孢杆菌yitJ SAM-1核糖开关功能的构象和运动知之甚少。因此，我们使用单分子Förster共振能量转移（smFRET）显微镜和隐式马尔可夫模型分析，探索了其构象能图随Mg ²⁺和SAM配体浓度的变化。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 ²⁺依赖的分数种群和构象动力学，包括状态寿命，相互转化率系数和平衡时标。具有终止子和抗终止子折叠的核糖开关并存，而SAM结合仅使种群逐渐向终止子状态转移。我们观察到SAM结合时构象转变的明显加速，这对于下游基因表达之前的短暂决策窗口中的转换可能至关重要。