title: Substrate shape preference of Escherichia coli ribonuclease P ribozyme and holo enzyme using bottom-half part-shifting variants of pre-tRNA.
abstract: We showed previously that the bacterial ribonuclease P (RNase P) ribozyme has substrate shape preference depending on the concentrations of catalytically important magnesium ions. The ribozyme discriminates a canonical cloverleaf precursor tRNA from a hairpin RNA with a CCA-tag sequence at low concentrations of magnesium ions. By detailed analysis of the shape preference using the bottom-half part-shifting variants of a tRNA precursor, we showed that the RNAs in a T-shape structure can be substrates for the ribozyme reactions even at low concentrations of magnesium ions, and that the RNA in a natural L-shape is the best substrate for both the ribozyme and the holo enzyme. The results also showed that the position of the bottom-half part did not affect the cleavage site selection of a substrate by the enzyme. Our results are the first kinetic evidence to show the importance of the bottom-half part of tRNA molecule, and our result also showed that the holo enzyme can discriminate substrate shape as well as the ribozyme at low concentrations of metal ions.
authors.affiliation: Division of Bioscience and Biotechnology, Department of Ecological Engineering, Toyohashi University of Technology, Toyohashi, Aichi, Japan. tanakat@eco.tut.ac.jp
authors.forename: Terumichi
authors.initials: T
authors.lastname: Tanaka
authors.forename: Yasuhiro
authors.initials: Y
authors.lastname: Nagai
authors.forename: Yo
authors.initials: Y
authors.lastname: Kikuchi
mesh_terms: D029968:Escherichia coli Proteins / Q000378:metabolism*; D020035:Holoenzymes / Q000378:metabolism*; D007700:Kinetics; D008274:Magnesium; D009690:Nucleic Acid Conformation; D012322:RNA Precursors / Q000737:chemistry / Q000378:metabolism*; D016337:RNA, Catalytic / Q000378:metabolism; D043262:Ribonuclease P / Q000378:metabolism*; D013379:Substrate Specificity
chemical_list: D029968:Escherichia coli Proteins; D020035:Holoenzymes; D012322:RNA Precursors; D016337:RNA, Catalytic; D043262:Ribonuclease P; D008274:Magnesium