Folding of a transcriptionally acting preQ1 riboswitch.
7-Aminomethyl-7-deazaguanine (preQ(1)) sensitive mRNA domains belong to the smallest riboswitches known to date. Although recent efforts have revealed the three-dimensional architecture of the ligand-aptamer complex less is known about the molecular details of the ligand-induced response mechanism that modulates gene expression. We present an in vitro investigation on the ligand-induced folding process of the preQ(1) responsive RNA element from Fusobacterium nucleatum using biophysical methods, including fluorescence and NMR spectroscopy of site-specifically labeled riboswitch variants. We provide evidence that the full-length riboswitch domain adopts two different coexisting stem-loop structures in the expression platform. Upon addition of preQ(1), the equilibrium of the competing hairpins is significantly shifted. This system therefore, represents a finely tunable antiterminator/terminator interplay that impacts the in vivo cellular response mechanism. A model is presented how a riboswitch that provides no obvious overlap between aptamer and terminator stem-loop solves this communication problem by involving bistable sequence determinants.
Rieder
Ulrike
U
Institute of Organic Chemistry and Center for Molecular Biosciences, University of Innsbruck, Innrain 52a, 6020 Innsbruck, Austria.
Kreutz
Christoph
C
Micura
Ronald
R
D052157:Aptamers, Nucleotide / Q000737:chemistry / Q000235:genetics / Q000378:metabolism; D001483:Base Sequence; D016967:Fusobacterium nucleatum / Q000235:genetics / Q000378:metabolism; D007700:Kinetics; D008024:Ligands; D009682:Magnetic Resonance Spectroscopy; D008958:Models, Molecular; D009690:Nucleic Acid Conformation; D011744:Pyrimidinones / Q000737:chemistry* / Q000378:metabolism; D011758:Pyrroles / Q000737:chemistry* / Q000378:metabolism; D012329:RNA, Bacterial / Q000737:chemistry* / Q000235:genetics / Q000378:metabolism; D012333:RNA, Messenger / Q000737:chemistry* / Q000235:genetics / Q000378:metabolism; D013050:Spectrometry, Fluorescence
C096876:7-(aminomethyl)-7-deazaguanine; D052157:Aptamers, Nucleotide; D008024:Ligands; D011744:Pyrimidinones; D011758:Pyrroles; D012329:RNA, Bacterial; D012333:RNA, Messenger