Mn(2+)-sensing mechanisms of yybP-ykoY orphan riboswitches.
Publication Type:Journal Article
Source:Mol Cell, Volume 57, Issue 6, p.1110-1123 (2015)
Keywords:Adenosine Triphosphatases, Bacillus subtilis, Base Sequence, Crystallography, X-Ray, Escherichia coli, Gene Expression Regulation, Bacterial, Lactococcus lactis, Magnesium, Models, Molecular, Molecular Sequence Data, Mutagenesis, Site-Directed, Mutation, Nucleic Acid Conformation, Quorum Sensing, Regulatory Sequences, Ribonucleic Acid, Riboswitch, RNA, Bacterial
<p>Gene regulation in cis by riboswitches is prevalent in bacteria. The yybP-ykoY riboswitch family is quite widespread, yet its ligand and function remained unknown. Here, we characterize the Lactococcus lactis yybP-ykoY orphan riboswitch as a Mn(2+)-dependent transcription-ON riboswitch, with a ∼30-40 μM affinity for Mn(2+). We further determined its crystal structure at 2.7 Å to elucidate the metal sensing mechanism. The riboswitch resembles a hairpin, with two coaxially stacked helices tethered by a four-way junction and a tertiary docking interface. The Mn(2+)-sensing region, strategically located at the highly conserved docking interface, has two metal binding sites. Whereas one site tolerates the binding of either Mg(2+) or Mn(2+), the other site strongly prefers Mn(2+) due to a direct contact from the N7 of an invariable adenosine. Mutagenesis and a Mn(2+)-free E. coli yybP-ykoY structure further reveal that Mn(2+) binding is coupled with stabilization of the Mn(2+)-sensing region and the aptamer domain. </p>