Coevolution of RNA and protein subunits in RNase P and RNase MRP, two RNA processing enzymes

Abstract

RNase P and RNase mitochondrial RNA processing (MRP) are ribonucleoproteins (RNPs) that consist of a catalytic RNA and a varying number of protein cofactors. RNase P is responsible for precursor tRNA maturation in all three domains of life, while RNase MRP, exclusive to eukaryotes, primarily functions in rRNA biogenesis. While eukaryotic RNase P is associated with more protein cofactors and has an RNA subunit with fewer auxiliary structural elements compared to its bacterial cousin, the double-anchor precursor tRNA recognition mechanism has remarkably been preserved during evolution. RNase MRP shares evolutionary and structural similarities with RNase P, preserving the catalytic core within the RNA moiety inherited from their common ancestor. By incorporating new protein cofactors and RNA elements, RNase MRP has established itself as a distinct RNP capable of processing ssRNA substrates. The structural information on RNase P and MRP helps build an evolutionary trajectory, depicting how emerging protein cofactors harmonize with the evolution of RNA to shape different functions for RNase P and MRP. Here, we outline the structural and functional relationship between RNase P and MRP to illustrate the coevolution of RNA and protein cofactors, a key driver for the extant, diverse RNP world.

Keywords: RNase MRP; RNase P; coevolution; cryo-EM; ribonucleoprotein.

Figure 1

Coevolution of RNA and protein in RNase P and MRP. An evolutionary tree depicting the hypothetical pathway of how RNase P and MRP have developed from the last universal common ancestor (LUCA). Bacterial and archaeal RNase P variants employ two RNA-based anchors, the T-loop anchor and A anchor, for tRNA recognition. The A anchor is substituted with the Pop1-aided anchor in eukaryotic RNase P, whereas the double-anchor mechanism not used in RNase MRP. The substrate pool of eukaryotic RNase P and MRP has driven the coevolution of their RNAs and protein cofactors. Representative holoenzyme structures use PDB 3Q1Q (Thermotoga maritima RNase P), PDB 6K0A (Methanococcus jannaschii RNase P), PDB 6AGB (Saccharomyce cerevisiae RNase P), and PDB 7C79 (Saccharomyce cerevisiae RNase MRP). MRP, mitochondrial RNA processing.

Figure 2

Biological roles of RNase P and MRP.A, schematic illustrating the processing of pre-tRNAs by RNase P across three domains of life. The diagram depicts the organization of rDNA genes and tRNA genes along with the positions of RNase P cleavage sites. The middle panel specifically represents a common organization found in the Euryarchaeota, one of the largest archaeal phyla and characterized by a typical bacterial operon organization. B and C, RNase MRP is involved in ribosome biogenesis, cell cycle regulation, mitochondrial R-loop processing, and other important biological processes in yeast (B) and human (C). RNase MRP cleaves the ITS1_A3 site of pre-rRNA in yeast (B) and involves at least one step in the processing cascade of human pre-rRNA (C). Yeast RNase MRP processes CLB2 mRNA and CTS1 mRNA in their 5′ UTRs for cell cycle regulation (B). Human RNase MRP cleaves mitochondrial RNA to generate a primer for DNA replication in mitochondria (C). CLB2, cyclin B2; MRP, mitochondrial RNA processing; pre-tRNA, precursor tRNA.

Figure 3

Coevolution model of RNase P.A, secondary structure diagrams of RNase P RNAs. Top panel: representative RNase P RNA secondary structures of bacterial types A, B, and C. Middle panel: secondary structures of archaeal type A, M, and P RPRs. Bottom panel: yeast and human RPR secondary structures. All protein components are colored and placed in positions according to their respective structures. B, stacked representation of RNase Ps from the three domains of life. Different RNA elements are colored. C, secondary structure diagram of yeast telomerase RNA TLC1. RPR, RNase P RNA.

Figure 4

pre-tRNA recognition by RNase P from three domains of life.A–C, double-anchor mechanism of bacterial RNase P (Escherichia coli) (A), archaeal RNase P (Methanococcus jannaschii, monomer) (B), eukaryotic RNase P (C). One anchor consists of conserved T-loops formed by CR-II and CR-III, the other anchor is an adenosine in bacteria and archaea, and the coiled loop η1 of Pop1 in eukarya. In each complex, only the RPR, two anchors, and the pre-tRNA substrate are shown as cartoons. Close-up views of the two anchors are shown in boxes at the right. CR, conserved region; Pre-tRNA, precursor tRNA.

Figure 5

RNase P and MRP catalytic mechanism.A, schematic models for the shared catalytic mechanisms of RNase P and MRP. Conserved RNA architecture orchestrates the presence of two Mg²⁺ ions at the catalytic core. B, the common two-metal ion mechanism of the phosphodiester bond cleavage reaction and proton transfer pathway of RNA processing in RNase P and MRP. MRP, mitochondrial RNA processing.

Figure 6

Structural comparison between yeast RNase P and MRP.A and B, structures of yeast RNase P RNA Rpr1 (A) and RNase MRP RNA Nme1 (B). Left: secondary structure diagrams of Rpr1 (A) and Nme1 (B). Structural elements are denoted in different colors. The C and S domains are labeled. Right: tertiary structures of Rpr1 (A) and Nme1 (B). C, structural superposition analysis of the universally conserved pseudoknot formed by CR-I-IV-V between Rpr1 and Nme1. These regions are colored the same as in A and B. D, superposition of Rpr1 and Nme1 helical cores in two orthogonal views. Rpr1 is colored the same as in A and Nme1 colored in light gray. E, structural comparison of substrate recognition by RNase MRP and RNase P. Left: the single-stranded ITS1_A3 substrate lies in the pocket and is recognized by Nme1, Pop4_NTM, Pop1_NTM, and Rmp1. Middle: the pre-tRNA substrate is recognized by two anchors. Right: structural superposition analysis of active sites in RNase MPP and RNase P reveals that the single-stranded ITS1_A3 substrate adopts a helical-like conformation resembling the 5′ strand of the pre-tRNA acceptor stem in RNase P. C domain, catalytic domain; MRP, mitochondrial RNA processing; Pop1_NTM, Pop1 N-terminal motif; Pre-tRNA, precursor tRNA; S domain, specificity domain.