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Riboswitches01:56

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Shine-Dalgarno Accessibility Governs Ribosome Binding to the Adenine Riboswitch.

Julius Blechar1, Vanessa de Jesus1, Boris Fürtig1

  • 1Institute for Organic Chemistry and Chemical Biology, Center for Biomolecular Magnetic Resonance, Johann Wolfgang Goethe-University Frankfurt, Max-von-Laue-Straße 7, 60438 Frankfurt am Main, Germany.

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Adenine-sensing riboswitches control gene expression by altering RNA structure. This study reveals that adenine binding increases ribosome binding site accessibility, with ribosomal protein S1 further enhancing this effect for efficient gene regulation.

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Area of Science:

  • Molecular Biology
  • RNA Biology
  • Gene Regulation

Background:

  • Translational riboswitches regulate gene expression by modulating ribosome binding site (RBS) accessibility through ligand-induced conformational changes.
  • Understanding these dynamic structural changes is crucial for deciphering gene regulatory mechanisms.

Purpose of the Study:

  • To investigate the adenine-sensing riboswitch in *Vibrio vulnificus*.
  • To quantify changes in RBS accessibility between ligand-free (apo) and ligand-bound (adenine-bound) states.
  • To elucidate the role of ribosomal protein S1 in riboswitch regulation.

Main Methods:

  • Employed single-molecule colocalization techniques: Single-Molecule Kinetic Analysis of RNA Transient Structure (SiM-KARTS) and Single-Molecule Kinetic Analysis of Ribosome Binding (SiM-KARB).
  • Utilized microscale thermophoresis (MST) to analyze ligand binding and conformational changes.
  • Determined kinetic rate constants for ribosome binding and riboswitch state transitions.

Main Results:

  • Both SiM-KARTS and SiM-KARB accurately report RBS accessibility in the adenine-sensing riboswitch.
  • Adenine binding significantly increases RBS accessibility, transitioning the riboswitch to an 'ON' state.
  • Ribosomal protein S1 promotes unwinding of RNA secondary structures, enhancing ribosome binding in the apo state.

Conclusions:

  • Adenine binding to the riboswitch increases RBS accessibility, facilitating translation initiation.
  • Ribosomal protein S1 plays a key role in priming the riboswitch for ribosome binding.
  • The rapid ribosome binding kinetics compared to riboswitch state transitions ensure efficient regulatory decisions.