Article abstract

Nature Structural & Molecular Biology 14, 308 - 317 (2007)
Published online: 25 March 2007 | doi:10.1038/nsmb1224

A riboswitch selective for the queuosine precursor preQ1 contains an unusually small aptamer domain

Adam Roth1, Wade C Winkler2,5, Elizabeth E Regulski2, Bobby W K Lee4, Jinsoo Lim2, Inbal Jona2, Jeffrey E Barrick1,3,5, Ankita Ritwik2, Jane N Kim2, Rüdiger Welz2, Dirk Iwata-Reuyl4 & Ronald R Breaker1,2,3

A previous bioinformatics-based search for riboswitches yielded several candidate motifs in eubacteria. One of these motifs commonly resides in the 5' untranslated regions of genes involved in the biosynthesis of queuosine (Q), a hypermodified nucleoside occupying the anticodon wobble position of certain transfer RNAs. Here we show that this structured RNA is part of a riboswitch selective for 7-aminomethyl-7-deazaguanine (preQ1), an intermediate in queuosine biosynthesis. Compared with other natural metabolite-binding RNAs, the preQ1 aptamer appears to have a simple structure, consisting of a single stem-loop and a short tail sequence that together are formed from as few as 34 nucleotides. Despite its small size, this aptamer is highly selective for its cognate ligand in vitro and has an affinity for preQ1 in the low nanomolar range. Relatively compact RNA structures can therefore serve effectively as metabolite receptors to regulate gene expression.

  1. Howard Hughes Medical Institute, Yale University, P.O. Box 208103, New Haven, Connecticut 06520-8103, USA.
  2. Department of Molecular, Cellular and Developmental Biology, Yale University, P.O. Box 208103, New Haven, Connecticut 06520-8103, USA.
  3. Department of Molecular Biophysics and Biochemistry, Yale University, P.O. Box 208103, New Haven, Connecticut 06520-8103, USA.
  4. Department of Chemistry, Portland State University, P.O. Box 751, Portland, Oregon 97207, USA.
  5. Present addresses: Department of Biochemistry, The University of Texas Southwestern Medical Center, Dallas, Texas 75390-9038, USA (W.C.W.) and Department of Microbiology and Molecular Genetics, Michigan State University, East Lansing, Michigan 48824, USA (J.E.B.).

Correspondence to: Ronald R Breaker1,2,3 e-mail:


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