Abstract: TheyybP-ykoYfamily, a common type of riboswitch in bacteria, can sensitively detect the concentration of Mn2+. A novel pH response element was discovered in the 5′-UTR region of theE.coli alxgene containing one of the conserved sequences of theyybPriboswitch. Based on structural predictions, theE.coli yybPriboswitch is structurally similar to the known riboswitch located on the upstream of theyoaBgene inLactococcus lactis, suggesting that Mn2+ binding site may also locate at L1 and L3 ring. However, the current studies on theyybPriboswitch aptamer domain ofE.colifocused on static analysis; thus conformational changes after binding with Mn2+ under different pH conditions are still unclear. In this study, a SHAPE chemical detection method was used to analyze conformational differences before and after binding with Mn2+ at different pH (pH 6.0, 7.0, 8.0) for theyybPriboswitch aptamer domain. The results confirmed that L1 and L3 rings of theyybPriboswitch aptamer domain were Mn2+ binding sites, and the change of pH in solution did not affect the capability of theyybPriboswitch to bind Mn2+. The whole nucleic acid skeleton of P1 and P2 of theyybPriboswitch folded into a compact double helix at pH 8.0. In summary, Mn2+ binds theyybPriboswitch under alkaline conditions made its structure more stable, which was presumably conducive to the regulation of the downstreamalxgenes byyybPriboswitch, and provided a theoretical basis for the subsequent study of the mechanism of action of the riboswitch.

Key words: yybP riboswitch, aptamer domain, SHAPE chemical detection method, Mn²+, pH