title: Mn(2+)-sensing mechanisms of yybP-ykoY orphan riboswitches.
abstract: 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.
authors: Department of Molecular Biology and Genetics, Cornell University, 253 Biotechnology Building, Ithaca, NY 14853, USA.
authors: Ian R
authors: IR
authors: Price
authors: Department of Microbiology, Wing Hall, Cornell University, Ithaca, NY 14853, USA.
authors: Ahmed
authors: A
authors: Gaballa
authors: Department of Molecular Biology and Genetics, Cornell University, 253 Biotechnology Building, Ithaca, NY 14853, USA.
authors: Fang
authors: F
authors: Ding
authors: Department of Microbiology, Wing Hall, Cornell University, Ithaca, NY 14853, USA.
authors: John D
authors: JD
authors: Helmann
authors: Department of Molecular Biology and Genetics, Cornell University, 253 Biotechnology Building, Ithaca, NY 14853, USA. Electronic address: ailong.ke@cornell.edu.
authors: Ailong
authors: A
authors: Ke
mesh_terms: D000251:Adenosine Triphosphatases / Q000235:genetics / Q000378:metabolism; D001412:Bacillus subtilis / Q000187:drug effects / Q000235:genetics; D001483:Base Sequence; D018360:Crystallography, X-Ray; D004926:Escherichia coli / Q000235:genetics* / Q000378:metabolism; D015964:Gene Expression Regulation, Bacterial; D013294:Lactococcus lactis / Q000235:genetics* / Q000378:metabolism; D008274:Magnesium / Q000378:metabolism* / Q000633:toxicity; D008958:Models, Molecular; D008969:Molecular Sequence Data; D016297:Mutagenesis, Site-Directed; D009154:Mutation; D009690:Nucleic Acid Conformation; D053038:Quorum Sensing; D012329:RNA, Bacterial / Q000737:chemistry* / Q000235:genetics / Q000378:metabolism; D038621:Regulatory Sequences, Ribonucleic Acid; D058928:Riboswitch / Q000502:physiology*
chemical_list: D012329:RNA, Bacterial; D038621:Regulatory Sequences, Ribonucleic Acid; D058928:Riboswitch; D000251:Adenosine Triphosphatases; D008274:Magnesium