title: E88, a new cyclic-di-GMP class I riboswitch aptamer from Clostridium tetani, has a similar fold to the prototypical class I riboswitch, Vc2, but differentially binds to c-di-GMP analogs.
abstract: C-di-GMP has emerged as a ubiquitous second messenger, which regulates the transition between sessile and motile lifestyles and virulence factor expression in many pathogenic bacteria using both RNA riboswitches and protein effectors. We recently showed that two additional class I c-di-GMP riboswitch aptamers (Ct-E88 and Cb-17B) bind c-di-GMP with nanomolar affinity, and that Ct-E88 RNA binds 2'-F-c-di-GMP 422 times less tightly than class I Vc2 RNA. Based on sequence comparison, it was concluded that the global folds of Ct-E88 and Vc2 RNAs were similar and that differences in ligand binding were probably due to differences in binding site architectures. Herein, we utilized EMSA, aptamer sensing spinach modules, SAXS and 1D NMR titration to study the conformational transitions of Ct-E88. We conclude that whereas the global folds of the bound states of Vc2 and Ct-E88 RNAs are similar, the unbound states are different and this could explain differences in ligand affinities between these class I c-di-GMP riboswitches.
authors.affiliation: Department of Chemistry and Biochemistry, University of Maryland, College Park, MD 20742, USA. dayie@umd.edu hsintim@umd.edu.
authors.forename: Yiling
authors.initials: Y
authors.lastname: Luo
authors.forename: Bin
authors.initials: B
authors.lastname: Chen
authors.forename: Jie
authors.initials: J
authors.lastname: Zhou
authors.forename: Herman O
authors.initials: HO
authors.lastname: Sintim
authors.forename: T Kwaku
authors.initials: TK
authors.lastname: Dayie
mesh_terms: D052157:Aptamers, Nucleotide / Q000737:chemistry / Q000378:metabolism*; D001483:Base Sequence; D003017:Clostridium tetani / Q000235:genetics / Q000378:metabolism*; D006152:Cyclic GMP / Q000031:analogs & derivatives* / Q000737:chemistry / Q000378:metabolism; D008958:Models, Molecular; D008969:Molecular Sequence Data; D019906:Nuclear Magnetic Resonance, Biomolecular; D009690:Nucleic Acid Conformation; D059370:RNA Folding; D012329:RNA, Bacterial / Q000737:chemistry / Q000378:metabolism*; D058928:Riboswitch / Q000502:physiology*; D016415:Sequence Alignment
chemical_list: D052157:Aptamers, Nucleotide; D012329:RNA, Bacterial; D058928:Riboswitch; C062025:bis(3',5')-cyclic diguanylic acid; D006152:Cyclic GMP