Sequence analysis of RNase MRP RNA reveals its origination from eukaryotic RNase P RNA

Abstract

RNase MRP is a eukaryote-specific endoribonuclease that generates RNA primers for mitochondrial DNA replication and processes precursor rRNA. RNase P is a ubiquitous endoribonuclease that cleaves precursor tRNA transcripts to produce their mature 5' termini. We found extensive sequence homology of catalytic domains and specificity domains between their RNA subunits in many organisms. In Candida glabrata, the internal loop of helix P3 is 100% conserved between MRP and P RNAs. The helix P8 of MRP RNA from microsporidia Encephalitozoon cuniculi is identical to that of P RNA. Sequence homology can be widely spread over the whole molecule of MRP RNA and P RNA, such as those from Dictyostelium discoideum. These conserved nucleotides between the MRP and P RNAs strongly support the hypothesis that the MRP RNA is derived from the P RNA molecule in early eukaryote evolution.

FIGURE 1.

Comparison of the secondary structures of RNase MRP and RNase P RNAs from hemiascomycetes. Boldface letters represent the universally conserved nucleotides for P RNA and MRP RNA, respectively. The degenerate nucleotides are shown according to (Cornish-Bowden 1985). A dot represents any nucleotide. Two parallel straight lines represent a helix, and a curved line represents a loop containing a variable number of nucleotides. The P7 helix with a question mark in MRP RNA indicates it is not defined (see main text). A P7.2 helix insertion in the MRP structure of S. paradoxus is not included. The nomenclature for these conserved regions (CRs) is that of (Chen and Pace 1997). Helix numbering follows their putative homology with bacterial structures (Haas et al. 1994). The P RNA structure model is derived from (Kachouri et al. 2005), while the insertions are shown with arrows.

FIGURE 2.

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FIGURE 2.

Sequence conservation in the catalytic domains of RNase P RNA and MRP RNA. Conserved nucleotides between MRP and P RNA are marked. The 5′ ends of the sequences are denoted with a small circle. (A) The P15 helix; (B) the P19 helix; (C) the internal loop of P3 helix is 100% conserved between P and MRP RNAs from C. glabrata, as indicated in boldface letters.

FIGURE 3.

Sequence conservation in the specificity domain of RNase P RNA and MRP RNA. Marked are the conserved nucleotides for P RNA and MRP RNA from the same species. The 5′ ends of the sequences are denoted with a small circle. (A) The P8 helix. Boldface letters in E. cuniculi show that the P8 of P RNA is identical to that of MRP RNA; (B) the P9 helix; (C) the P7.2 helix.

FIGURE 4.

The secondary structure of P and MRP RNAs from D. discoideum. Conserved nucleotides are found along the entire sequence of P RNA and MRP RNA. The 5′ ends of the sequences are denoted with a small circle. The boldface letters represent the universally conserved regions (CR I to CR V). The nomenclature for these conserved regions (CRs) is that of (Chen and Pace 1997). Helix numbering follows their putative homology with bacterial structures (Haas et al. 1994).