Structural basis for ligand recognition in the tobramycin riboswitch

Area of Science:

• Molecular Biology
• Synthetic Biology
• Structural Biology

Background:

• A novel tobramycin-responsive riboswitch was engineered using Capture-SELEX and in vivo screening.
• This riboswitch exhibits high dynamic range, ligand affinity, and selectivity in regulating translation initiation in eukaryotes.
• Its distinct secondary structure suggests a novel mechanism for aminoglycoside recognition.

Purpose of the Study:

• To elucidate the structural basis for the high regulatory efficiency and ligand selectivity of the tobramycin riboswitch.
• To characterize the RNA-ligand complex structure using high-resolution nuclear magnetic resonance (NMR) spectroscopy.

Main Methods:

• High-resolution solution nuclear magnetic resonance (NMR) spectroscopy was employed to determine the structure of the riboswitch in complex with tobramycin.
• Comparative structural analysis was performed between the ligand-bound and free forms of the riboswitch.

Main Results:

• The study revealed a novel structural organization for an aminoglycoside-binding RNA motif, characterized by unique intermolecular interactions.
• A distinctive pattern of hydrogen bonds and electrostatic interactions was observed between the RNA and all three rings of tobramycin.
• Ligand binding induces extensive noncanonical RNA-RNA interactions, explaining the high ligand affinity and exceptional switching efficiency.

Conclusions:

• The determined structure provides a molecular rationale for the remarkable performance of the synthetic tobramycin riboswitch.
• The findings highlight a novel mode of aminoglycoside recognition and RNA-ligand interaction.
• This work lays the foundation for designing more sophisticated synthetic regulatory RNA elements.