RNA structure influences numerous processes in all organisms. In bacteria, these processes include transcription termination and attenuation, small RNA and protein binding, translation initiation, and mRNA stability, and can be regulated via metabolite availability and other stresses. Here we use Structure-seq2 to probe the in vivo RNA structurome of Bacillus subtilis grown in the presence and absence of amino acids. Our results reveal that amino acid starvation results in lower overall dimethyl sulfate (DMS) reactivity of the transcriptome, indicating enhanced protection owing to protein binding or RNA structure. Starvation-induced changes in DMS reactivity correlated inversely with transcript abundance changes. This correlation was particularly pronounced in genes associated with the stringent response and CodY regulons, which are involved in adaptation to nutritional stress, suggesting that RNA structure contributes to transcript abundance change in regulons involved in amino acid metabolism. Structure-seq2 accurately reported on four known amino acid-responsive riboswitches: T-box, SAM, glycine, and lysine riboswitches. Additionally, we discovered a transcription attenuation mechanism that reduces yfmG expression when amino acids are added to the growth medium. We also found that translation of a leader peptide (YfmH) encoded just upstream of yfmG regulates yfmG expression. Our results are consistent with a model in which a slow rate of yfmH translation caused by limitation of the amino acids encoded in YfmH prevents transcription termination in the yfmG leader region by favoring formation of an overlapping antiterminator structure. This novel RNA switch offers a way to simultaneously monitor the levels of multiple amino acids.

中文翻译：

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氨基酸饥饿时 RNA 结构的 Structure-seq2 探测揭示了枯草芽孢杆菌中已知和新的 RNA 转换

RNA 结构影响所有生物体的许多过程。在细菌中，这些过程包括转录终止和衰减、小 RNA 和蛋白质结合、翻译起始和 mRNA 稳定性，并且可以通过代谢物可用性和其他压力进行调节。在这里，我们使用 Structure-seq2 来探测在存在和不存在氨基酸的情况下生长的枯草芽孢杆菌的体内 RNA 结构组。我们的结果表明，氨基酸饥饿导致转录组的总体硫酸二甲酯 (DMS) 反应性降低，表明由于蛋白质结合或 RNA 结构增强了保护。饥饿引起的 DMS 反应性变化与转录本丰度变化成反比。这种相关性在与严格反应和 CodY 调节子相关的基因中尤为明显，参与对营养压力的适应，表明 RNA 结构有助于参与氨基酸代谢的调节子的转录本丰度变化。Structure-seq2 准确报告了四种已知的氨基酸响应核糖开关：T-box、SAM、甘氨酸和赖氨酸核糖开关。此外，我们发现了一种转录衰减机制，当将氨基酸添加到生长培养基中时，该机制会降低 yfmG 的表达。我们还发现在 yfmG 上游编码的前导肽 (YfmH) 的翻译调节 yfmG 表达。我们的结果与模型一致，在该模型中，由于 YfmH 中编码的氨基酸的限制导致 yfmH 翻译速度缓慢，通过有利于形成重叠的抗终止子结构来防止 yfmG 前导区的转录终止。