title: Multiple substrate binding sites in the ribozyme from Bacillus subtilis RNase P.
abstract: The ribozyme from Bacillus subtilis RNase P (P RNA) recognizes an RNA structure consisting of the acceptor stem and the T stem-loop of tRNA substrates. An in vitro selection experiment was carried out to obtain potential RNA substrates that may interact with the P RNA differently from the tRNA substrate. Using a P RNA-derived ribozyme that contains most, if not all, of the structural elements thought to be involved in active site formation of P RNA, but lacks the putative binding site for the T stem-loop of tRNA, a single RNA substrate was isolated after nine rounds of selection. This RNA is a competent substrate for the ribozyme used in selection as well as for the full-length P RNA. Biochemical characterization shows that this selected substrate interacts at a different site compared with the tRNA substrate. The selection experiment also identified a self-cleaving RNA seemingly different from other known ribozymes. These results indicate that a biological ribozyme can contain different binding sites for different RNA substrates. This alternate binding site model suggests a simple mechanism for evolving existing ribozymes to recognize RNA substrates of diverse structures.
authors.affiliation: Department of Biochemistry and Molecular Biology, University of Chicago, IL 60637, USA.
authors.forename: T
authors.initials: T
authors.lastname: Pan
authors.forename: M
authors.initials: M
authors.lastname: Jakacka
mesh_terms: D001412:Bacillus subtilis / Q000201:enzymology*; D001483:Base Sequence; D004722:Endoribonucleases / Q000378:metabolism*; D006868:Hydrolysis; D008969:Molecular Sequence Data; D009690:Nucleic Acid Conformation; D016337:RNA, Catalytic / Q000737:chemistry / Q000378:metabolism*; D043262:Ribonuclease P; D013379:Substrate Specificity
chemical_list: D016337:RNA, Catalytic; D004722:Endoribonucleases; D043262:Ribonuclease P