Ligand-induced folding of the adenosine deaminase A-riboswitch and implications on riboswitch translational control

Renate Rieder, Kathrin Lang, Dagmar Graber, Ronald Micura

Research output: Contribution to journalArticlepeer-review

155 Scopus citations

Abstract

By using a structure-based fluorescence spectroscopic approach, we have examined the folding of an adenine-responsive riboswitch that regulates translation initiation. We observed adaptive recognition of the ligand for the aptamer domain of adenosine deaminase (add) mRNA from Vibrio vulnificus, and revealed pronounced conformational changes even in the preorganized loop-loop region that is distant from the binding site. Importantly, the full-length riboswitch domain, which has a potential translational repressor stem is able to form a binary complex with adenine, and does not act as a folding trap to inhibit binding. The aptamer that is extended by the expression platform therefore remains fully responsive to its ligand; this is in contrast to the previously investigated pbuE A-riboswitch, which becomes trapped in a nonresponsive terminator fold. Consequently, the latter must employ complex response mechanisms, such as operating in kinetic-control mode or using transcriptional pausing, to provide time for the aptamer portion to fold and to bind. The different behavior of the riboswitches can be rationalized by their distinct sequence interface between the aptamer and expression platform. For the add A-riboswitch, our data suggest a thermodynamically driven response mechanism.

Original languageEnglish
Pages (from-to)896-902
Number of pages7
JournalChemBioChem
Volume8
Issue number8
DOIs
StatePublished - 25 May 2007
Externally publishedYes

Keywords

  • Aminopurine
  • Folding
  • Induced fit
  • Ligand effects
  • RNA
  • Riboswitches

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