title: DNA-rescuable allosteric inhibition of aptamer II ligand affinity by aptamer I element in the shortened Vibrio cholerae glycine riboswitch.
abstract: Glycine riboswitches contain two aptamers and turn on the expression of downstream genes in bacteria. Although full-length glycine riboswitches were shown to exhibit no glycine-binding cooperativity, the truncated glycine riboswitches were confirmed to bind two glycine molecules cooperatively. Thorough understanding of the ligand-binding cooperativity may shed light on the molecular basis of the cooperativity and help design novel intricate biosensing genetic circuits for application in synthetic biology. A previously proposed sequential model does not readily provide explanation for published data showing a deleterious mutation in the first aptamer inhibiting the glycine binding of the second one. Using the glycine riboswitch from Vibrio cholerae as a model system, we have identified a region in the first aptamer that modulates the second aptamer function especially in the shortened glycine riboswitch. Importantly, this modulation can be rescued by the addition of a complementary oligodeoxynucleotide, demonstrating the feasibility of developing this system into novel genetic circuits that sense both glycine and a DNA signal.
authors.affiliation: Department of Chemistry, University of Central Florida, Orlando, FL 32816, USA.
authors.forename: Eileen M
authors.initials: EM
authors.lastname: Sherman
authors.affiliation: Department of Chemistry, University of Central Florida, Orlando, FL 32816, USA.
authors.forename: Galal
authors.initials: G
authors.lastname: Elsayed
authors.affiliation: Department of Chemistry, University of Central Florida, Orlando, FL 32816, USA.
authors.forename: Jackie M
authors.initials: JM
authors.lastname: Esquiaqui
authors.affiliation: Department of Chemistry, University of Central Florida, Orlando, FL 32816, USA.
authors.forename: Mohammed
authors.initials: M
authors.lastname: Elsayed
authors.affiliation: Department of Chemistry, University of Central Florida, Orlando, FL 32816, USA.
authors.forename: Bryan
authors.initials: B
authors.lastname: Brinda
authors.affiliation: Department of Chemistry, University of Central Florida, Orlando, FL 32816, USA yejingdong@gmail.com.
authors.forename: Jing-Dong
authors.initials: JD
authors.lastname: Ye
mesh_terms: D000494:Allosteric Regulation; D052157:Aptamers, Nucleotide / Q000235:genetics* / Q000378:metabolism; D001483:Base Sequence; D004247:DNA / Q000378:metabolism; D005998:Glycine / Q000235:genetics / Q000378:metabolism*; D008024:Ligands; D009690:Nucleic Acid Conformation; D012333:RNA, Messenger / Q000235:genetics; D058928:Riboswitch / Q000235:genetics*; D014734:Vibrio cholerae / Q000235:genetics*
chemical_list: D052157:Aptamers, Nucleotide; D008024:Ligands; D012333:RNA, Messenger; D058928:Riboswitch; D004247:DNA; D005998:Glycine
keywords: allosteric control; aptamer; cooperativity; genetic circuit; glycine riboswitch
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