Abstract
RNase P, a ribozyme-based ribonucleoprotein (RNP) complex that catalyzes tRNA 5′-maturation, is ubiquitous in all domains of life, but the evolution of its protein components (RNase P proteins, RPPs) is not well understood. Archaeal RPPs may provide clues on how the complex evolved from an ancient ribozyme to an RNP with multiple archaeal and eukaryotic (homologous) RPPs, which are unrelated to the single bacterial RPP. Here, we analyzed the sequence and structure of archaeal RPPs from over 600 available genomes. All five RPPs are found in eight archaeal phyla, suggesting that these RPPs arose early in archaeal evolutionary history. The putative ancestral genomic loci of archaeal RPPs include genes encoding several members of ribosome, exosome, and proteasome complexes, which may indicate coevolution/coordinate regulation of RNase P with other core cellular machineries. Despite being ancient, RPPs generally lack sequence conservation compared to other universal proteins. By analyzing the relative frequency of residues at every position in the context of the high-resolution structures of each of the RPPs (either alone or as functional binary complexes), we suggest residues for mutational analysis that may help uncover structure-function relationships in RPPs.
Highlights
RNase P, a ubiquitous endonuclease responsible for tRNA 51 maturation in all three domains of life [1,2,3,4,5,6,7], functions as one of two distinct scaffolds: either a ribozyme-based ribonucleoprotein (RNP) or an RNA-free, proteinaceous form [4,8,9]; here, we focus on the RNP
P RNP variants is exemplified by the association of a single catalytic RNase P RNA (RPR) with one, five, and ten RNase P protein (RPP) subunits in Bacteria, Archaea, and Eukarya, respectively
To gain some insight into possible predecessors that eventually led to the higher protein:RNA ratio in archaeal and eukaryotic RNase P, we examined the large number of archaeal genomes available and used the resulting inventory of archaeal RPPs to analyze the evolution and structure of the protein subunits of archaeal RNase P
Summary
RNase P, a ubiquitous endonuclease responsible for tRNA 51 maturation in all three domains of life [1,2,3,4,5,6,7], functions as one of two distinct scaffolds: either a ribozyme-based ribonucleoprotein (RNP) or an RNA-free, proteinaceous form [4,8,9]; here, we focus on the RNP. Using polyclonal antisera individually raised against Methanothermobacter thermautotrophicus (Mth) RPP21, RPP29, POP5, and RPP30, which were first identified based on the corresponding yeast/human homologs, tRNA 51 maturation activity was immunoprecipitated from a partially purified Mth RNase P preparation [19]. This finding inspired us and others to pursue biochemical reconstitutions of Mth, Pyrococcus furiosus (Pfu), Pyrococcus horikoshii (Pho), Methanocaldococcus jannaschii (Mja), and Methanococcus maripaludis (Mma) RNase P [22,24,25,26,27,35,36,39]. We report here that this scenario is unlikely based on our analysis of a large collection of archaeal genomes, and we provide additional insights on the evolution and structure of archaeal RNase P
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