Eukaryotic ribonuclease P: increased complexity to cope with the nuclear pre-tRNA pathway

Abstract

Ribonuclease P is an ancient enzyme that cleaves pre-tRNAs to generate mature 5' ends. It contains an essential RNA subunit in Bacteria, Archaea, and Eukarya, but the degree to which the RNA subunit relies on proteins to supplement catalysis is highly variable. The eukaryotic nuclear holoenzyme has recently been found to contain almost twenty times the protein content of the bacterial enzymes, in addition to having split into at least two related enzymes with distinct substrate specificity. In this review, recent progress in understanding the molecular architecture and functions of nuclear forms of RNase P will be considered.

Fig. 1

Predicted secondary structure of yeast nuclear RNase P RNA. Nucleotides that are most conserved in bacterial, archaeal and eukaryotic RNase P RNAs are marked with asterisks (Frank et al., 2000). Five critical regions (“CR”s) are numbered according to the Chen and Pace nomenclature (Chen and Pace, 1997), and correspond to clusters of the most conserved positions. “P” represents helical regions, with numbers assigned based on corresponding bacterial structures (Haas et al., 1994). The P4 helix is marked with brackets connected by a line. Nucleotides within the shaded regions are protected from nuclease attack in the holoenzyme compared to deproteinized RNA (Tranguch et al., 1994). For technical reasons it is not known whether the last 26 nucleotides are protected by protein in the holoenzyme. (Figure adapted from Tranguch et al., 1994).

Fig. 2

Subnuclear localization of yeast nuclear RNase P. A fluorescent oligonucleotide probe complementary to the RPR1 RNA subunit (green) was hybridized to fixed, permeabilized yeast. Yeast were stained with DAPI (blue in aH panels) to show the nucleoplasm and a fluorescent oligonucleotide to a small nucleolar RNA (U14, red in the second and third panels). The DAPI nucleoplasm signal and position of U14 in the nucleolus are as expected. The RPRJ RNA probe localizes more than 70% in or near the nucleolus, with secondary punctate loci that are somewhat variable among strains. Cytoplasmic features are not visible with these fluorescent tags. (Figure adapted from Bertrand et al., 1998).