Unusually High‐Affinity Mg²⁺ Binding at the AU‐Rich Sequence within the Antiterminator Hairpin of a Mg²⁺ Riboswitch

Abstract

Mg2+-Responsive riboswitches represent a fascinating example of bifunctional RNAs that sense Mg2+ ions with high selectivity and autonomously regulate the expression of Mg2+-transporter proteins. The mechanism of the mgtA riboswitch is scarcely understood, and a detailed structural analysis is called for to study how this RNA can selectively recognize Mg2+ and respond by switching between two alternative stem loop structures. In this work, we investigated the structure and Mg2+-binding properties of the lower part of the antiterminator loop C from the mgtA riboswitch of Yersinia enterocolitica by solution NMR and report a discrete Mg2+-binding site embedded in the AU-rich sequence. At the position of Mg2+ binding, the helical axis exhibits a distinct kink accompanied by a widening of the major groove, which accommodates the Mg2+-binding pocket. An unusually large overlap between two adenine residues on the opposite strands suggests that the bending may be sequence-induced by strong stacking interactions, enabling Mg2+ to bind at this so-far not described metal-ion binding site.

NMR structure of the 5′ splice site in the group IIB intron Sc.ai5γ—conformational requirements for exon–intron recognition

“…S4). G•C base pairs but also A•U tracks have been shown previously to bind divalent ions (Korth and Sigel 2012;Sigel and Sigel 2013). In the following, we now focus our analysis of the chemical shift changes on the 11-nt loop region and their comparison in the absence and in the presence of IBS1 (Fig.…”

Increasing intracellular magnesium levels with the 31-amino acid MgtS protein

“…To evaluate the cause of the defect, we created a reporter for intracellular Mg 2+ levels by fusing lacZ to the Mg 2+ -responsive 5′-untranslated region (UTR) of E. coli mgtA. Depending on the intracellular Mg 2+ concentration, the mgtA 5′-UTR has been shown to adopt alternative RNA secondary structures, which modulates transcription elongation into the mgtA ORF through sequestration of a Rho-dependent transcription terminator (19)(20)(21). Specifically, elongation into mgtA is increased when free intracellular Mg 2+ levels are low, whereas the transcript is terminated in the 5′-UTR when Mg 2+ levels are high.…”

RNA Regulators: Formidable Modulators of Yersinia Virulence

“…A bioinformatics analysis predicted a few conserved riboswitches (Moco, FMN, cobalamin, yybP-ykoY element), the characterized Mg 2+ -responsive riboswitch mgtA [39], and 17 additional riboswitch-like elements, indicating that the Yersinia riboswitch-repertoire still remains undiscovered. Recently, a powerful unbiased high-throughput approach for global discovery of riboswitches and attenuators (Term-seq) has been described [40].…”