McCown Phillip J, Corbino Keith A, Stav Shira, Sherlock Madeline E, Breaker Ronald R
Department of Molecular, Cellular and Developmental Biology, Yale University, New Haven, Connecticut 06520-8103, USA.
Howard Hughes Medical Institute, Yale University, New Haven, Connecticut 06520-8103, USA.
RNA. 2017 Jul;23(7):995-1011. doi: 10.1261/rna.061234.117. Epub 2017 Apr 10.
Riboswitches are commonly used by bacteria to detect a variety of metabolites and ions to regulate gene expression. To date, nearly 40 different classes of riboswitches have been discovered, experimentally validated, and modeled at atomic resolution in complex with their cognate ligands. The research findings produced since the first riboswitch validation reports in 2002 reveal that these noncoding RNA domains exploit many different structural features to create binding pockets that are extremely selective for their target ligands. Some riboswitch classes are very common and are present in bacteria from nearly all lineages, whereas others are exceedingly rare and appear in only a few species whose DNA has been sequenced. Presented herein are the consensus sequences, structural models, and phylogenetic distributions for all validated riboswitch classes. Based on our findings, we predict that there are potentially many thousands of distinct bacterial riboswitch classes remaining to be discovered, but that the rarity of individual undiscovered classes will make it increasingly difficult to find additional examples of this RNA-based sensory and gene control mechanism.
核糖开关通常被细菌用于检测多种代谢物和离子，以调节基因表达。迄今为止，已发现了近40种不同类型的核糖开关，它们经过实验验证，并在与同源配体结合的复合物中以原子分辨率进行了建模。自2002年首次发表核糖开关验证报告以来的研究结果表明，这些非编码RNA结构域利用许多不同的结构特征来创建对其靶标配体具有极高选择性的结合口袋。一些核糖开关类型非常常见，几乎存在于所有谱系的细菌中，而其他类型则极为罕见，仅出现在少数已对DNA进行测序的物种中。本文展示了所有经过验证的核糖开关类型的共有序列、结构模型和系统发育分布。基于我们的研究结果，我们预测可能仍有成千上万种不同的细菌核糖开关类型有待发现，但由于单个未发现类型的稀有性，将越来越难以找到这种基于RNA的传感和基因控制机制的更多实例。
