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Escherichia coli yybP-ykoY Riboswitch as a Tandem Riboswitch Regulated by Mn2+ and pH
Wenwen Xiao1, Guangfeng Liu2, Ting Chen1
1College of Biological Science and Medical Engineering, Donghua University, Shanghai 201620, China.
ACS Chemical Biology
|April 19, 2025
Summary
The Escherichia coli yybP-ykoY riboswitch uses Mn2+ and pH to control gene expression. Manganese binding triggers a switch to an ON state in alkaline conditions, enabling precise environmental adaptation.
Area of Science:
- Molecular Biology
- Structural Biology
- Biochemistry
Background:
- The yybP-ykoY riboswitch in Escherichia coli regulates translation of mntP and alx genes.
- This riboswitch features two tandem domains sensitive to manganese (Mn2+) and pH.
- Understanding its structural dynamics is key to deciphering gene regulation.
Purpose of the Study:
- To investigate the tertiary structure and conformational dynamics of the E. coli yybP-ykoY riboswitch.
- To elucidate the role of Mn2+ and pH in riboswitch-mediated gene regulation.
- To determine the binding sites for divalent metal ions.
Main Methods:
- X-ray crystallography was used to determine the aptamer domain structure.
- Small-angle X-ray scattering (SAXS) provided insights into overall conformation.
- Chemical probing (SHAPE) assessed RNA accessibility and dynamics.
Main Results:
- The crystal structure revealed a coaxial superhelix with a three-way junction, forming a pocket for Mg2+ and Mn2+ binding.
- SAXS and SHAPE probing showed pH-independent conformation without Mn2+.
- Significant conformational changes were observed under alkaline conditions with Mn2+ present.
Conclusions:
- Mn2+ binding induces an OFF-to-ON state transition in alkaline conditions, regulating gene expression.
- The riboswitch exhibits a finely tuned adaptive response to environmental changes.
- This mechanism allows for sophisticated control over gene expression based on metal ion and pH levels.
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