Folding of the SAM aptamer is determined by the formation of a K-turn-dependent pseudoknot

Biochemistry. 2008 Feb 12;47(6):1490-9. doi: 10.1021/bi701164y. Epub 2008 Jan 19.

Abstract

The S-adenosylmethionine (SAM) riboswitch is one of the most recurrent riboswitches found in bacteria and has three known different natural aptamers. The Bacillus subtilis yitJ SAM riboswitch aptamer is organized around a four-way junction which is characterized by the presence of a pseudoknot and a K-turn motif. By replacing the adenine involved in a Watson-Crick base pair at position 138 in the core region of the aptamer with the fluorescent analogue 2-aminopurine (2AP), we show that the ligand-induced reorganization of the aptamer strongly attenuates 2AP fluorescence. The fluorescence quenching process is specific to SAM on the basis of the observation that the structural analogue S-adenosylhomocysteine does not promote a similar effect. We find that the pseudoknot is important for the reorganization of the core domain and that the K-turn motif also has a marked influence on the core domain reorganization, most probably through its important role in pseudoknot formation. Finally, we show that SAM riboswitch ligand binding is facilitated by the L7Ae K-turn binding protein, which suggests that K-turn motifs may be protein anchor sites used by riboswitches to promote RNA folding.

Publication types

  • Research Support, Non-U.S. Gov't

MeSH terms

  • Aptamers, Nucleotide / chemistry*
  • Base Sequence
  • Models, Molecular
  • Molecular Sequence Data
  • Nucleic Acid Conformation*
  • S-Adenosylmethionine / chemistry*
  • Spectrometry, Fluorescence

Substances

  • Aptamers, Nucleotide
  • S-Adenosylmethionine