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bioRxiv · 10.64898/2026.02.18.706685

pH-dependent allosteric remodeling of a bacterial riboswitch couples alkaline activation to metal sensing

Palmer, D.·Chauvier, A.·Silva, T. F. D.·Ontiveros, A.·Bussi, G.·Walter, N. G.·Mishanina, T. V.
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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 E. coli alx riboswitch distinctively couples Mn2+ sensing to cytoplasmic alkalinity, but the mechanism is unknown. We show that pH tunes the alx aptamers 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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Palmer, D., Chauvier, A., Silva, T. F. D., Ontiveros, A., Bussi, G., Walter, N. G., Mishanina, T. V.. 2026-02-19. pH-dependent allosteric remodeling of a bacterial riboswitch couples alkaline activation to metal sensing. https://doi.org/10.64898/2026.02.18.706685

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