Substrate Recognition and Specificity of a Minimal Protein-Only RNase P

Abstract

tRNAs are typically transcribed with extended 5’ and 3’ ends that must be removed before they attain their active form. One of the first steps of tRNA processing in nearly every organism is the removal of the 5’ leader sequence by ribonuclease P (RNase P). This work investigates a newly discovered class of RNase P enzymes, Homologs of Aquifex RNase P (HARPs). In contrast to other RNase Ps, HARPs consist only of a metallonuclease domain and lack the substrate recognition domains essential in other classes of RNase P enzymes. Determination of the cryo-EM structure of A. aeolicus HARP (Aq880) and two crystal structures of H. thermophilus HARP (Hth1307) reveal that both enzymes form large ring-like assemblies: a dodecamer in Aq880 and a tetradecamer in Hth1307. In both oligomers, the enzyme active site is 42 Å away from a positively charged helical region, as seen in other protein-only RNase P enzymes, which likely serves to recognize and bind the elbow region of the pre-tRNA substrate. In addition, native mass spectrometry (MS) was used to confirm and characterize the previously unreported tetradecamer state. Notably, multiple oligomeric states of Hth1307 are able to cleave pre-tRNAs. Furthermore, single-turnover kinetic studies indicate that Hth1307 cleaves pre-tRNAs from multiple species with a preference for native substrates. These data provide a closer look at the nuanced similarities and differences in tRNA processing across disparate classes of RNase P.