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 some of the RNase MRP proteins shared with RNase P undergo an unexpected RNA-driven remodeling that allows them to bind to divergent RNAs. Further, we reveal how this RNA-driven protein remodeling, acting together with the introduction of new auxiliary elements, results in the functional diversification of RNase MRP and its progenitor, RNase P, and demonstrate structural underpinnings of the acquisition of new functions by catalytic RNPs.

Fig. 1. RNA components of RNase MRP and RNase P.

The catalytic (C-) domains of the two related enzymes are similar both in their secondary structures and in their folds, whereas the specificity (S-) domains are distinct. a, b Secondary structure diagrams of the RNase MRP and RNase P RNAs, respectively. c, d Folding of the RNase MRP and RNase P RNAs, respectively, color coded as in (a, b).

Fig. 2. Structure of the RNase MRP holoenzyme.

Protein components (shown as surfaces) are color coded as marked; the RNA elements (shown as a cartoon) are color coded according to Fig. 1a.

Fig. 3. RNA-protein interactions in RNase MRP.

a The structure of the conserved element 5′-GA(G/A)A(G/A)-3′ (nucleotides 109–113) and its interactions with protein Pop1 (red). The 5′-GA(G/A)A(G/A)-3′ element folds into a GNRA tetraloop capping stem P8, with the last purine (A113) bulging out. A113 is observed in both syn- and anti- conformations; the syn- conformation appears to be stabilized by a stacking interaction with the conserved Arg107 of protein Pop1. b–e Loop L5 of the S-domain caps the P5 stem. The loop is devoid of the base pairs; its structure is stabilized by interactions with protein components Pop4 (green) and Snm1 (blue).

Fig. 4. Proteins Pop1 and Pop4 stabilize the overall RNase MRP RNA structure and undergo RNA-driven remodeling.

a Interactions of Pop1 (red), Pop6 (gray), and Pop7 (pale green) with RNase MRP RNA (gray). b, c The fold of the N-terminal part of Pop1 in RNase MRP differs from that in RNase P. The N-terminal parts of Pop1 are shown in red; the similarly folded C-terminal parts of Pop1 are shown in gray. Interactions of Pop4 (green) with the RNA components of RNase MRP (d) and RNase P (e). RNA elements are marked and color coded according to Fig. 1a, b. The part of the Pop4 α3 helix that folds differently in RNase MRP and RNase P is boxed.

Fig. 5. Interactions of protein Rmp1 with the RNA component of RNase MRP.

a–d Rmp1 binds at the foundation of the P15 helical stem, in the vicinity of the catalytic center, interacting with stems P4, P9, and the J7/9 junction. Interactions of Rmp1 with RNase MRP RNA result in a change of the P15 stem orientation compared to that observed in RNase P.

Fig. 6. Substrate binding pockets in RNase MRP and RNase P.

Protein components are color coded according to Fig. 2. RNase MRP and RNase P RNAs are shown as cartoons in black. The substrate pre-tRNA in the substrate binding pocket of RNase P (b) is shown as a cartoon in yellow. The location of the scissile bonds is shown by yellow spheres (a, b). The locations of the RNase MRP nucleotides that crosslink to substrates are shown as spheres in cyan (a).