Structural and dynamic mechanisms for coupled folding and tRNA recognition of a translational T-box riboswitch

• Published in: Nature communications Vol. 14; no. 1; pp. 7394 - 14
• Main Authors: Niu, Xiaolin, Xu, Zhonghe, Zhang, Yufan, Zuo, Xiaobing, Chen, Chunlai, Fang, Xianyang
• Format: Journal Article
• Language: English
• Published: London Nature Publishing Group UK 15.11.2023; Nature Publishing Group; Nature Portfolio
• Subjects: 119/118; 631/337/2179; 631/45/500; 631/535/1261; 631/57/2265; Aptamers; BASIC BIOLOGICAL SCIENCES; Binding; Conformation; Docking; Folding; Gene regulation; Grooves; Humanities and Social Sciences; Magnesium; multidisciplinary; Ribonucleic acid; Riboswitches; RNA; SAXS; Science; Science (multidisciplinary); Single-molecule biophysics; Transfer RNA; Translation; tRNA
• ISSN: 2041-1723; 2041-1723
• DOI: 10.1038/s41467-023-43232-z

T-box riboswitches are unique riboregulators where gene regulation is mediated through interactions between two highly structured RNAs. Despite extensive structural insights, how RNA-RNA interactions drive the folding and structural transitions of T-box to achieve functional conformations remains unclear. Here, by combining SAXS, single-molecule FRET and computational modeling, we elaborate the folding energy landscape of a translational T-box aptamer consisting of stems I, II and IIA/B, which Mg 2+ -induced global folding and tRNA binding are cooperatively coupled. smFRET measurements reveal that high Mg 2+ stabilizes IIA/B and its stacking on II, which drives the pre-docking of I and II into a competent conformation, subsequent tRNA binding promotes docking of I and II to form a high-affinity tRNA binding groove, of which the essentiality of IIA/B and S-turn in II is substantiated with mutational analysis. We highlight a delicate balance among Mg 2+ , the intra- and intermolecular RNA-RNA interactions in modulating RNA folding and function. T-box riboswitches are RNA-based gene regulators, composed of highly structured noncoding RNAs: the T-box and a tRNA ligand. Here, the authors assess the folding of a translational T-box aptamer and dissect the role of Mg 2+ , intra- and intermolecular RNA-RNA interactions in modulating its folding and function.