ArticleNucleic acids research2026
pH-dependent allosteric remodeling of a bacterial riboswitch couples alkaline activation to metal sensing.
Article in Nucleic acids research, 2026. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Not yet cited in PubMed.
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Abstract
The widespread yybP-ykoY riboswitches control bacterial manganese (Mn) homeostasis by activating exporter expression in response to intracellular Mn2+ levels. The Escherichia coli alx riboswitch distinctively couples Mn2+ sensing to cytoplasmic alkalinity, but the mechanism is unknown. We show that pH tunes the alx aptamer's conformational sampling to modulate Mn2+ sensitivity. Single-molecule FRET reveals that Mn2+ stabilizes a docked three-way-junction conformation, and alkaline pH shifts this equilibrium to sensitize metal-dependent folding. Molecular dynamics simulations identify a loop whose low-pH-induced base pairing perturbs the adjacent helix, predicted to allosterically disrupt the Mn2+-binding state. In vivo reporters indicate that both this loop and the Mn2+-binding core are required for optimal pH-dependent translational activation: replacing the core with the non-pH-responsive mntP sequence abolishes activation. These results define how RNA allosterically integrates orthogonal metal and proton cues to enable combinatorial environmental sensing during alkaline stress.
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