title: Differential substrate recognition by isozymes of plant protein-only Ribonuclease P.
abstract: Ribonuclease P (RNase P) catalyzes the cleavage of leader sequences from precursor tRNA (pre-tRNA). Typically, these enzymes are ribonucleic protein complexes that are found in all domains of life. However, a new class of RNase P has been discovered that is composed entirely of protein, termed protein-only RNase P (PRORP). To investigate the molecular determinants of PRORP substrate recognition, we measured the binding affinities and cleavage kinetics of Arabidopsis PRORP1 for varied pre-tRNA substrates. This analysis revealed that PRORP1 does not make significant contacts within the trailer or beyond N-1of the leader, indicating that this enzyme recognizes primarily the tRNA body. To determine the extent to which sequence variation within the tRNA body modulates substrate selectivity and to provide insight into the evolution and function of PRORP enzymes, we measured the reactivity of the three Arabidopsis PRORP isozymes (PRORP1-3) with four pre-tRNA substrates. A 13-fold range in catalytic efficiencies (10(4)-10(5)M(-1)s(-1)) was observed, demonstrating moderate selectivity for pre-tRNA substrates. Although PRORPs bind the different pre-tRNA species with affinities varying by as much as 100-fold, the three isozymes have similar affinities for a given pre-tRNA, suggesting similar binding modes. However, PRORP isozymes have varying degrees of cleavage fidelity, which is dependent on the pre-tRNA species and the presence of a 3'-discriminator base. This work defines molecular determinants of PRORP substrate recognition that provides insight into this new class of RNA processing enzymes.
authors.affiliation: Department of Biological Chemistry, University of Michigan, Ann Arbor, Michigan 48109, USA.
authors.forename: Michael J
authors.identifier: http://orcid.org/0000-0001-9990-930X
authors.initials: MJ
authors.lastname: Howard
authors.affiliation: Department of Biochemistry and Molecular Biology, Uniformed Services University of the Health Sciences, Bethesda, Maryland 20814, USA.
authors.forename: Agnes
authors.initials: A
authors.lastname: Karasik
authors.affiliation: Department of Biological Chemistry, University of Michigan, Ann Arbor, Michigan 48109, USA.
authors.forename: Bradley P
authors.initials: BP
authors.lastname: Klemm
authors.affiliation: Department of Microbiology and Immunology, University of Michigan, Ann Arbor, Michigan 48109, USA.
authors.forename: Christine
authors.initials: C
authors.lastname: Mei
authors.affiliation: Department of Biochemistry and Molecular Biology, Uniformed Services University of the Health Sciences, Bethesda, Maryland 20814, USA.
authors.forename: Aranganathan
authors.initials: A
authors.lastname: Shanmuganathan
authors.affiliation: Department of Biological Chemistry, University of Michigan, Ann Arbor, Michigan 48109, USA Department of Chemistry, University of Michigan, Ann Arbor, Michigan 48109, USA.
authors.forename: Carol A
authors.initials: CA
authors.lastname: Fierke
authors.affiliation: Department of Biochemistry and Molecular Biology, Uniformed Services University of the Health Sciences, Bethesda, Maryland 20814, USA.
authors.forename: Markos
authors.initials: M
authors.lastname: Koutmos
mesh_terms: D017360:Arabidopsis / Q000201:enzymology; D007527:Isoenzymes / Q000378:metabolism*; D007700:Kinetics; D010940:Plant Proteins / Q000378:metabolism*; D043262:Ribonuclease P / Q000378:metabolism*; D013379:Substrate Specificity
chemical_list: D007527:Isoenzymes; D010940:Plant Proteins; D043262:Ribonuclease P
keywords: PRORP; RNase P; fidelity; isozymes; tRNA