Riboswitch regulates critical pathways in bacteria, fungi and plants. The yybP-ykoY motif composes most common riboswitch classes. A novel pH-responsive RNA element containing yybP-ykoY consensus sequence in the 5′untranslated region of alx gene in Escherichia coli. Its ligand and regulation mechanism are not understood. Here we characterize this yybP-ykoY motif as a Mn2+- dependent transcription-ON yybP riboswitch. Our 3.8 Å crystal structure explains the mechanism of metal sensing. The Mn2+-binding core of the Escherichia coli is similar with the previously determined L. lactis yybP-ykoY riboswitch structure, suggesting these two Mn2+- dependent riboswitches utilize a highly conserved ligand-recognition mechanism. We used SHAPE (selective 2′-hydroxyl acylation analyzed by primer extension) chemical probing analysis to further determine the anti-termination activity was related to aptamer domain conformational changes inducing by Mn2+ binding. Mutagenesis revealed that certain modifications in the Mn2+-binding core lead to loss of Mn2+ binding and anti-termination, which suggests that the Mn2+ binding related to stabilization of the Mn2+sensing region.

Mn2+-sensing and conformational switching mechanism in the Escherichia coli Mn2+-dependent riboswitch

255th National Meeting (2018)

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