title: Functional coupling between a distal interaction and the cleavage site in bacterial RNase-P-RNA-mediated cleavage.
abstract: Bacterial RNase P consists of one protein and one RNA [RNase P RNA (RPR)]. RPR can process tRNA precursors correctly in the absence of the protein. Here we have used model hairpin loop substrates corresponding to the acceptor, T-stem, and T-loop of a precursor tRNA to study the importance of the T-loop structure in RPR-alone reaction. T-stem/loop (TSL) interacts with a region in RPR [TSL binding site (TBS)], forming TSL/TBS interaction. Altering the T-loop structure affects both cleavage site selection and rate of cleavage at the correct site +1 and at the alternative site -1. The magnitude of variation depended on the structures of the T-loop and the TBS region, with as much as a 150-fold reduction in the rate of cleavage at +1. Interestingly, for one T-loop structure mutant, no difference in the rate at -1 was detected compared to cleavage of the substrate with an unchanged T-loop, indicating that, in this case, the altered T-loop structure primarily influences events required for efficient cleavage at the correct site +1. We also provide data supporting a functional link between a productive TSL/TBS interaction and events at the cleavage site. Collectively, our findings emphasize the interplay between separate regions upon formation of a productive RPR substrate that leads to efficient and accurate cleavage. These new data provide support for an induced-fit mechanism in bacterial RPR-mediated cleavage at the correct site +1.
authors.affiliation: Department of Cell and Molecular Biology, Biomedical Center, Box 596, SE-751 24 Uppsala, Sweden.
authors.forename: Shiying
authors.initials: S
authors.lastname: Wu
authors.forename: Yu
authors.initials: Y
authors.lastname: Chen
authors.forename: Magnus
authors.initials: M
authors.lastname: Lindell
authors.forename: Guanzhong
authors.initials: G
authors.lastname: Mao
authors.forename: Leif A
authors.initials: LA
authors.lastname: Kirsebom
mesh_terms: D001426:Bacterial Proteins / Q000378:metabolism*; D004926:Escherichia coli / Q000737:chemistry / Q000201:enzymology* / Q000378:metabolism; D007700:Kinetics; D008958:Models, Molecular; D009690:Nucleic Acid Conformation; D012322:RNA Precursors / Q000737:chemistry / Q000378:metabolism; D012329:RNA, Bacterial / Q000737:chemistry / Q000378:metabolism*; D043262:Ribonuclease P / Q000737:chemistry / Q000378:metabolism*
chemical_list: D001426:Bacterial Proteins; D012322:RNA Precursors; D012329:RNA, Bacterial; D043262:Ribonuclease P