Characterization of RNA-based and protein-only RNases P from bacteria encoding both enzyme types

Abstract

A small group of bacteria encode two types of RNase P, the classical ribonucleoprotein (RNP) RNase P as well as the protein-only RNase P HARP (homolog ofAquifexRNaseP). We characterized the dual RNase P activities of five bacteria that belong to three different phyla. All five bacterial species encode functional RNA (genernpB) and protein (genernpA) subunits of RNP RNase P, but only the HARP of the thermophileThermodesulfatator indicus(phylum Thermodesulfobacteria) was found to have robust tRNA 5′-end maturation activity in vitro and in vivo in anEscherichia coliRNase P depletion strain. These findings suggest that both types of RNase P are able to contribute to the essential tRNA 5′-end maturation activity inT. indicus, thus resembling the predicted evolutionary transition state in the progenitor of the Aquificaceae before the loss ofrnpAandrnpBgenes in this family of bacteria. Remarkably,T. indicusRNase P RNA is transcribed with a P12 expansion segment that is posttranscriptionally excised in vivo, such that the major fraction of the RNA is fragmented and thereby truncated by ∼70 nt in the nativeT. indicushost as well as in theE. colicomplementation strain. Replacing the native P12 element ofT. indicusRNase P RNA with the short P12 helix ofThermotoga maritimaRNase P RNA abolished fragmentation, but simultaneously impaired complementation efficiency inE. colicells, suggesting that intracellular fragmentation and truncation ofT. indicusRNase P RNA may be beneficial to RNA folding and/or enzymatic activity.