Structural analysis of a class III preQ1 riboswitch reveals an aptamer distant from a ribosome-binding site regulated by fast dynamics

Proc Natl Acad Sci U S A. 2015 Jul 7;112(27):E3485-94. doi: 10.1073/pnas.1503955112. Epub 2015 Jun 23.


PreQ1-III riboswitches are newly identified RNA elements that control bacterial genes in response to preQ1 (7-aminomethyl-7-deazaguanine), a precursor to the essential hypermodified tRNA base queuosine. Although numerous riboswitches fold as H-type or HLout-type pseudoknots that integrate ligand-binding and regulatory sequences within a single folded domain, the preQ1-III riboswitch aptamer forms a HLout-type pseudoknot that does not appear to incorporate its ribosome-binding site (RBS). To understand how this unusual organization confers function, we determined the crystal structure of the class III preQ1 riboswitch from Faecalibacterium prausnitzii at 2.75 Å resolution. PreQ1 binds tightly (KD,app 6.5 ± 0.5 nM) between helices P1 and P2 of a three-way helical junction wherein the third helix, P4, projects orthogonally from the ligand-binding pocket, exposing its stem-loop to base pair with the 3' RBS. Biochemical analysis, computational modeling, and single-molecule FRET imaging demonstrated that preQ1 enhances P4 reorientation toward P1-P2, promoting a partially nested, H-type pseudoknot in which the RBS undergoes rapid docking (kdock ∼ 0.6 s(-1)) and undocking (kundock ∼ 1.1 s(-1)). Discovery of such dynamic conformational switching provides insight into how a riboswitch with bipartite architecture uses dynamics to modulate expression platform accessibility, thus expanding the known repertoire of gene control strategies used by regulatory RNAs.

Keywords: crystal structure; gene regulation; molecular dynamics; preQ1 riboswitch; single-molecule FRET.

Publication types

  • Research Support, Non-U.S. Gov't

MeSH terms

  • Aptamers, Nucleotide / chemistry
  • Aptamers, Nucleotide / genetics*
  • Aptamers, Nucleotide / metabolism
  • Base Sequence
  • Binding Sites / genetics
  • Clostridium / genetics
  • Clostridium / metabolism
  • Crystallography, X-Ray
  • Kinetics
  • Molecular Dynamics Simulation
  • Molecular Sequence Data
  • Nucleoside Q / chemistry
  • Nucleoside Q / metabolism
  • Pyrimidinones / chemistry
  • Pyrimidinones / metabolism
  • Pyrroles / chemistry
  • Pyrroles / metabolism
  • RNA Folding
  • RNA, Bacterial / chemistry
  • RNA, Bacterial / genetics*
  • RNA, Bacterial / metabolism
  • Ribosomes / genetics*
  • Ribosomes / metabolism
  • Riboswitch / genetics*
  • Thermodynamics


  • 7-(aminomethyl)-7-deazaguanine
  • Aptamers, Nucleotide
  • Pyrimidinones
  • Pyrroles
  • RNA, Bacterial
  • Riboswitch
  • Nucleoside Q

Associated data

  • PDB/5A39
  • PDB/5A3D