title: Roles of 5-substituents of tRNA wobble uridines in the recognition of purine-ending codons.
abstract: Many tRNA molecules that recognize the purine-ending codons but not the pyrimidine-ending codons have a modified uridine at the wobble position, in which a methylene carbon is attached directly to position 5 of the uracil ring. Although several models have been proposed concerning the mechanism by which the 5-substituents regulate codon-reading properties of the tRNAs, none could explain recent results of the experiments utilizing well-characterized modification-deficient strains of Escherichia coli. Here, we first summarize previous studies on the codon-reading properties of tRNA molecules with a U derivative at the wobble position. Then, we propose a hypothetical mechanism of the reading of the G-ending codons by such tRNA molecules that could explain the experimental results. The hypothesis supposes unconventional base pairs between a protonated form of the modified uridines and the G at the third position of the codon stabilized by two direct hydrogen bonds between the bases. The hypothesis also addresses differences between the prokaryotic and eukaryotic decoding systems.
authors: Cell-Free Science and Technology Research Center, Department of Applied Chemistry, Faculty of Engineering, Ehime University, 3, Bunkyo-cho, Matsuyama, Ehime 790-8577, Japan. takai@eng.ehime-u.ac.jp
authors: Kazuyuki
authors: K
authors: Takai
authors: Shigeyuki
authors: S
authors: Yokoyama
mesh_terms: D000926:Anticodon / Q000737:chemistry / Q000235:genetics*; D003062:Codon / Q000737:chemistry / Q000235:genetics*; D008957:Models, Genetic; D014176:Protein Biosynthesis; D011685:Purine Nucleotides / Q000737:chemistry / Q000235:genetics; D012343:RNA, Transfer / Q000737:chemistry / Q000235:genetics*; D013816:Thermodynamics; D014529:Uridine / Q000737:chemistry / Q000235:genetics*
chemical_list: D000926:Anticodon; D003062:Codon; D011685:Purine Nucleotides; D012343:RNA, Transfer; D014529:Uridine