Department of Chemistry, University of Konstanz, Universitätsstraße 10, 78457 Konstanz, Germany.
Bioinformatics Group, Department of Computer Science and Interdisciplinary Centre for Bioinformatics, Leipzig University, Härtelstraße 16-18, 04107 Leipzig, Germany.
Nucleic Acids Res. 2020 Dec 16;48(22):12889-12899. doi: 10.1093/nar/gkaa1102.
Riboswitches are RNAs that specifically sense a small molecule and regulate genes accordingly. The recent discovery of guanidine-binding riboswitches revealed the biological significance of this compound, and uncovered genes related to its biology. For example, certain sugE genes encode guanidine exporters and are activated by the riboswitches to reduce toxic levels of guanidine in the cell. In order to study guanidine biology and riboswitches, we applied a bioinformatics strategy for discovering additional guanidine riboswitches by searching for new candidate motifs associated with sugE genes. Based on in vitro and in vivo experiments, we determined that one of our six best candidates is a new structural class of guanidine riboswitches. The expression of a genetic reporter was induced 80-fold in response to addition of 5 mM guanidine in Staphylococcus aureus. This new class, called the guanidine-IV riboswitch, reveals additional guanidine-associated protein domains that are extremely rarely or never associated with previously established guanidine riboswitches. Among these protein domains are two transporter families that are structurally distinct from SugE, and could represent novel types of guanidine exporters. These results establish a new metabolite-binding RNA, further validate a bioinformatics method for finding riboswitches and suggest substrate specificities for as-yet uncharacterized transporter proteins.
Riboswitches 是一种能够特异性识别小分子并相应调节基因表达的 RNA。最近发现的胍结合型 riboswitches 揭示了该化合物的生物学意义，并揭示了与胍生物学相关的基因。例如，某些 sugE 基因编码胍外排蛋白，并被 riboswitches 激活，以降低细胞内胍的毒性水平。为了研究胍生物学和 riboswitches，我们应用了一种生物信息学策略，通过搜索与 sugE 基因相关的新候选基序来发现额外的胍 riboswitches。基于体外和体内实验，我们确定了我们的六个最佳候选者之一是胍 riboswitches 的一种新结构类别。在金黄色葡萄球菌中，加入 5mM 胍可诱导遗传报告基因表达增加 80 倍。这种新的胍-IV riboswitch 揭示了与以前建立的胍 riboswitches 极不相关或从未相关的额外胍相关蛋白结构域。这些蛋白结构域包括两种结构上不同于 SugE 的转运体家族，它们可能代表新型胍外排蛋白。这些结果建立了一种新的代谢物结合 RNA，进一步验证了寻找 riboswitches 的生物信息学方法，并为尚未表征的转运蛋白提供了底物特异性。
