Exploiting preQ(1) riboswitches to regulate ribosomal frameshifting

ACS Chem Biol. 2013 Apr 19;8(4):733-40. doi: 10.1021/cb300629b. Epub 2013 Jan 25.

Abstract

Knowing the molecular details of the interaction between riboswitch aptamers and their corresponding metabolites is important to understand gene expression. Here we report on a novel in vitro assay to study preQ(1) riboswitch aptamers upon binding of 7-aminomethyl-7-deazaguanine (preQ(1)). The assay is based on the ability of the preQ(1) aptamer to fold, upon ligand binding, into a pseudoknotted structure that is capable of stimulating -1 ribosomal frameshifting (-1 FS). Aptamers from three different species were found to induce between 7% and 20% of -1 FS in response to increasing preQ(1) levels, whereas preQ(1) analogues were 100-1000-fold less efficient. In depth mutational analysis of the Fusobacterium nucleatum aptamer recapitulates most of the structural details previously identified for preQ(1) aptamers from other bacteria by crystallography and/or NMR spectroscopy. In addition to providing insight into the role of individual nucleotides of the preQ(1) riboswitch aptamer in ligand binding, the presented system provides a valuable tool to screen small molecules against bacterial riboswitches in a eukaryotic background.

MeSH terms

  • Aptamers, Nucleotide
  • Base Sequence
  • Frameshifting, Ribosomal*
  • Nucleic Acid Conformation
  • Riboswitch*

Substances

  • Aptamers, Nucleotide
  • Riboswitch