PPR proteins shed a new light on RNase P biology

Abstract

A fast growing number of studies identify pentatricopeptide repeat (PPR) proteins as major players in gene expression processes. Among them, a subset of PPR proteins called PRORP possesses RNase P activity in several eukaryotes, both in nuclei and organelles. RNase P is the endonucleolytic activity that removes 5′ leader sequences from tRNA precursors and is thus essential for translation. Before the characterization of PRORP, RNase P enzymes were thought to occur universally as ribonucleoproteins, although some evidence implied that some eukaryotes or cellular compartments did not use RNA for RNase P activity. The characterization of PRORP reveals a two-domain enzyme, with an N-terminal domain containing multiple PPR motifs and assumed to achieve target specificity and a C-terminal domain holding catalytic activity. The nature of PRORP interactions with tRNAs suggests that ribonucleoprotein and protein-only RNase P enzymes share a similar substrate binding process.

Pentatricopeptide repeat motifs in the processing enzyme PRORP1 in Arabidopsis thaliana play a crucial role in recognition of nucleotide bases at TψC loop in precursor tRNAs

“…The crystal structure of T. maritima RNase P in complex with tRNA showed that A112 and G147 in the S-domain in RNase P RNA were arranged adjacent to G19 and C56 in the D and TwC loops, respectively [6]. Previously, cross-linking and mutational analyses suggested that G19 and C56 in tRNA Phe are involved in the interaction with PRORP1 [15,16]. It was therefore proposed that PRORP1 recognizes pre-tRNA in a similar manner to bacterial RNase Ps.…”

“…PRORP1 comprises five tandem pentatricopeptide repeat (PPR) motifs, a central linker domain, and a metallonuclease domain belonging to the NYN family [14]. Furthermore, cross-linking and mutational analyses suggested that G19 and C56 in tRNA are involved in the interaction with PRORP1 [15,16].…”

Footprinting analysis of interactions between the largest eukaryotic RNase P/MRP protein Pop1 and RNase P/MRP RNA components

“…The phylogenetically conserved RNA component of RNase P is the catalytic moiety of the enzyme (Guerrier-Takada et al 1983;Chen and Pace 1997;Pannucci et al 1999;Thomas et al 2000;Kikovska et al 2007;). In a number of cases, the ribonucleoprotein RNase P is supplemented or altogether replaced by unrelated protein-only enzymes termed PRORPs (Pinker et al 2013).…”

Determination of protein‐only RNase P interactome in Arabidopsis mitochondria and chloroplasts identifies a complex between PRORP1 and another NYN domain nuclease

“…More recently, this view was contradicted and the interest in RNase P renewed with the identification of a second type of RNase P in eukaryotes that was composed only of protein (Holzmann et al, 2008;Gobert et al, 2010;Pinker et al, 2013). This other type of RNase P, called PRORP for 'PROtein-only RNase P', was found in four out of five eukaryote supergroups, in organelles and/or in the nucleus (Lechner et al, 2015).…”