Ribonuclease (RNase) P is a universal RNA-based enzyme that is found in all kingdoms of life. RNase P is responsible for processing a number of RNA substrates including pre-tRNA and is involved in the regulation of transcription (Guerrier-Takada et al.
; Altman & Kirsebom, 1999
; Reiner et al.
; Kazantsev & Pace, 2006
; Coughlin et al.
). A typical RNase P consists of an RNA component which is responsible for catalysis and one or more protein components (Walker & Engelke, 2006
; Kikovska et al.
); all of the protein components are required for the activity of the enzyme in vivo
and are essential. The protein moiety of eubacterial RNase P contains one small protein, while archaeal RNase P has at least four proteins and eukaryotic RNase P has even more proteins (nine in Saccharomyces cerevisiae
RNase P). The reasons for the increased complexity of the more evolutionarily advanced RNases P are not clear (Walker & Engelke, 2006
; Marvin & Engelke, 2009
RNase MRP is a site-specific eukaryotic endoribonuclease (Chang & Clayton, 1987
). RNase MRP has several known functions in the cell. The vast majority of RNase MRP is located in the nucleolus, where it is involved in processing precursor ribosomal RNA (pre-rRNA; Lygerou et al.
; Lindahl et al.
). RNase MRP is also involved in regulating cell-cycle progression by cleaving the 5′-untranslated region (5′-UTR) of CLB2
mRNA, which encodes a B-type cyclin, thus triggering the degradation of this mRNA and aiding cell-cycle progression (Gill et al.
). RNase MRP is a universal eukaryotic enzyme which is required for the survival of the eukaryotic cell. RNase MRP closely resembles eukaryotic RNase P and consists of a presumably catalytic RNA component which shares multiple elements with RNase P as well as a number of protein components, most of which are found in both enzymes.
In S. cerevisiae
, RNases MRP and P share eight proteins: Pop1 (100.5 kDa; Lygerou et al.
), Pop3 (22.6 kDa; Dichtl & Tollervey, 1997
), Pop4 (32.9 kDa; Chu et al.
), Pop5 (19.6 kDa), Pop6 (18.2 kDa), Pop7 (15.8 kDa), Pop8 (15.5 kDa; Chamberlain et al.
) and Rpp1 (32.2 kDa; Stolc & Altman, 1997
). RNase MRP has two unique proteins [Snm1 (22.5 kDa; Schmitt & Clayton, 1994
) and Rmp1 (23.6 kDa; Salinas et al.
)], while RNase P has one unique protein, Rpr2 (16.3 kDa; Chamberlain et al.
), a homolog of Snm1. Similar to RNase P, all RNase MRP proteins are essential for the viability of the cell.
The RNA component of S. cerevisiae
RNase P is 369 nucleotides in length, while the RNA component of RNase MRP is 340 nucleotides in length. The secondary-structure elements which comprise the putative catalytic center are very similar in RNase P and RNase MRP. The results of a footprinting analysis indicate similar RNA–protein interactions in RNase MRP and eukaryotic RNase P (Esakova et al.
). The similarity between RNase MRP and eukaryotic RNase P strongly suggests that these enzymes have a common ancestor and share a catalytic mechanism but have evolved to have different specificities.
The structural organization of eukaryotic RNases P/MRP is not clear. There is no available structural information on any of their components.
The RNA components of RNases P and MRP have several well defined structural elements (Frank et al.
; Li et al.
; Walker & Avis, 2004
). The P3 domain of the RNA component (Fig. 1
) appears to play a unique and crucial role in RNase MRP and eukaryotic RNase P. It is found in practically all eukaryotic RNases P and RNases MRP but not in bacterial or archaeal enzymes. This domain is absolutely essential and is phylogenetically conserved (Lindahl et al.
; Ziehler et al.
). The P3 domain is expected to be a hub for protein binding in the eukaryotic enzymes of the RNase MRP/RNase P family, with several protein components, including Pop1, Pop6 and Pop7, binding to it (Ziehler et al.
; Perederina et al.
(a) The P3 domain of S. cerevisiae RNase MRP RNA; (b) a representative construct from the first set of P3-domain RNAs; (c) the construct from the second set of P3-domain RNAs which crystallized with the Pop6–Pop7 heterodimer.
The crystals reported here will be used to determine the molecular structure of the RNase MRP P3-domain RNA in a complex with RNase P/RNase MRP protein components Pop6 and Pop7 and will provide the first glimpse of the structural organization of the eukaryotic enzymes of the RNase P/RNase MRP family.