生物学杂志

生物学杂志 ›› 2025, Vol. 42 ›› Issue (3): 9-.doi: 10.3969/j.issn.2095-1736.2025.03.009

• 研究报告 • 上一篇    下一篇

碱性条件下yybP核糖开关结合Mn2+的构象分析

于莹莹， 冯姗姗， 肖雯雯， 陈　婷， 张云龙， 陆昌瑞   

  1. 东华大学 生物与医学工程学院， 上海 201620
  • 出版日期:2025-06-18 发布日期:2025-06-16
  • 通讯作者: 陆昌瑞，教授，研究方向为核酸与结构生物学，E-mail:crlu@dhu.edu.cn
  • 作者简介:于莹莹，硕士研究生，研究方向为核糖开关结构与功能，E-mail:yingyingyu0312@163.com
  • 基金资助:
    国家自然科学基金项目（82241010）； 上海市科学技术委员会基金项目（19410741800）； 上海市科学技术委员会基金项目（194110711000）

Conformational analysis of the yybP riboswitch binding to Mn2+ under alkaline conditions

YU Yingying, FENG Shanshan, XIAO Wenwen, CHEN Ting, ZHANG Yunlong, LU Changrui#br#   

  1. College of Biological Science and Medical Engineering, Donghua University, Shanghai 201620, China
  • Online:2025-06-18 Published:2025-06-16

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摘要： yybP-ykoY家族是细菌中常见的核糖开关类型，对Mn2+浓度具有高度敏感的监测能力。在大肠杆菌alx基因5′-UTR区含有一个包含yybP核糖开关保守序列的pH响应元件。根据结构预测，其与已知在乳酸乳球菌中位于yoaB基因上游的核糖开关结构类似，推测Mn2+结合位点可能也位于 L1、L3环。然而，目前大肠杆菌yybP核糖开关适体域的研究集中在静态解析上，对其在不同 pH 条件下结合Mn2+产生的构象变化尚不明确。通过运用SHAPE化学探测法对yybP核糖开关适体域在不同pH（pH 6.0、7.0和8.0）条件下与Mn2+结合前后的构象差异进行分析。结果证实了Mn2+结合位点位于L1和L3环处，并且在改变pH后，yybP核糖开关与Mn2+仍能结合；此外，在pH 8.0条件下，yybP核糖开关的P1、P2整体核酸骨架折叠成紧凑的双螺旋结构。综上结果表明，yybP核糖开关在碱性条件下与Mn2+结合后使其结构更加稳定，推测其有利于yybP核糖开关下游alx基因的调节，为后续研究该核糖开关的作用机制提供理论依据。

关键词: font-size:9.00pt, line-height:150%, ">font-size:9.00pt, line-height:150%, ">font-size:9.00pt, line-height:150%, ">yybPfont-size:10.00pt, line-height:150%, ">font-size:9.00pt, line-height:150%, ">核糖开关； 适体域； SHAPE化学探测法； Mn2+； pH

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

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