Cryo-EM structure of catalytic ribonucleoprotein complex RNase MRP

Abstract

RNase MRP is an essential eukaryotic ribonucleoprotein complex involved in the maturation of rRNA and the regulation of the cell cycle. RNase MRP is related to the ribozyme-based RNase P, but it has evolved to have distinct cellular roles. We report a cryo-EM structure of the S. cerevisiae RNase MRP holoenzyme solved to 3.0 Å. We describe the structure of this 450 kDa complex, interactions between its components, and the organization of its catalytic RNA. We show that while the catalytic center of RNase MRP is inherited from the ancestral enzyme RNase P, the substrate binding pocket of RNase MRP is significantly altered by the addition of unique RNA and protein elements, as well as by RNA-driven protein remodeling. One Sentence Summary:Changes in peripheral RNA elements and RNA-driven protein remodeling result in diversification of related catalytic RNPs 2 Main Text:Ribonuclease (RNase) MRP, a site-specific endoribonuclease, is a ribonucleoprotein complex (RNP) comprising a catalytic RNA moiety and multiple (ten in S. cerevisiae) protein components (1-4). RNase MRP is an essential eukaryotic enzyme that has been found in practically all eukaryotes analyzed (5). RNase MRP is localized to the nucleolus and, transiently, to the cytoplasm (3). Known RNase MRP functions include its participation in the maturation of rRNA and in the metabolism of specific mRNAs involved in the regulation of the cell cycle (6-13).Defects in RNase MRP result in a range of pleiotropic developmental disorders in humans (14).RNase MRP is evolutionarily related to RNase P, a ribozyme-based RNP primarily involved in the maturation of tRNA (15)(16)(17). RNase MRP appears to have split from the RNase P lineage early in the evolution of eukaryotes, acquiring distinct substrate specificity and cellular functions (5,18,19).The catalytic (C-) domain of RNase MRP RNA (Fig. 1A) has the secondary structure closely resembling that of the C-domain of RNase P (Figs. 1B) and includes elements forming a highly conserved catalytic core (3-5). The specificity (S-) domain of RNase MRP RNA does not have any apparent similarities with the S-domain of RNase P (Figs 1A, B). Crosslinking studies (20) indicate the involvement of the RNase MRP S-domain in substrate recognition.Most of the RNase MRP protein components are also found in eukaryotic RNase P (2). S.cerevisiae RNase MRP and RNase P share 8 proteins (Pop1, and Rpp1 (2 copies); RNase MRP protein Snm1 has a homologue in RNase P (Rpr2), while Rmp1 3 is found only in RNase MRP. Shared proteins bind to both C-and S-domains (21-23). RNase MRP proteins Pop1, Pop6, Pop7 are also an essential part of yeast telomerase, where they form a structural module that stabilizes the binding of telomerase components Est1 and Est2 (24).Here, we report a cryo-EM structure of the S. cerevisiae RNase MRP holoenzyme solved to the nominal resolution of 3.0 Å. We reveal the overall architecture of the RNP, the structural organization of its catalytic RNA moiety, the substrate binding pocket of the enzyme, and interactions between RN...

TREX reveals proteins that bind to specific RNA regions in living cells

“…Additionally, a prominently enriched protein among the identified ITS1 interactors was RPP25L (Fig. 5D and Dataset S8), a paralogue of RPP25, which constitutes a subunit of RMRP endonuclease complex (Perederina et al, 2020). This ribonucleoprotein complex facilitates the critical site 2 cleavage within the ITS1, separating the pre-40S and pre-60S processing particles during ribosome biogenesis (Goldfarb and Cech, 2017).…”

Coordination of transcription and processing of tRNA

“…Extensive biochemical purification analyses of nuclear RNase P from HeLa cells demonstrate that it consists of H1 RNA and many protein subunits, designated Rpp14, Rpp20, Rpp21, Rpp25, Rpp29, Rpp30, Rpp38, Rpp40, Pop1, and Pop5 (Table 1) [5,27,77,78,79]. Except for Rpp21, the remaining protein subunits are shared by RNase MRP, an evolutionary related nucleolar and mitochondrial ribonucleoprotein [28,31,78,79,80,81,82,83,84,85,86,87]. Elucidation of the tertiary structure of a highly purified HeLa RNase P by cryo-EM unveils that the catalytic H1 RNA is covered by its protein subunits arranged in three subcomplexes, Rpp20-Rpp25, Pop5-Rpp14-(Rpp30) 2 -Rpp40, and Rpp21-Rpp29-Rpp38, and a single polypeptide of Pop1 [29].…”