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.

The SARS-CoV-2 RNA–protein interactome in infected human cells

“…As the control, we used the endogenously expressed human ribonuclease mitochondrial RNA processing (RMRP) RNA and purified both SARS-CoV-2 RNA and RMRP from infected Huh7 cells. RMRP was selected for several reasons: (1) RMRP interacts with approximately ten well-known proteins that serve as an internal control 15 , 23 ; (2) RMRP is not translated; and (3) RMRP does not globally bind to mRNA. Hence, RMRP-binding proteins are distinct from the group of proteins expected to bind to SARS-CoV-2 RNAs, making it an ideal control for the discovery of unknown interactors.…”

“…As the control, we used the endogenously expressed human ribonuclease mitochondrial RNA processing (RMRP) RNA and purified both SARS-CoV-2 RNA and RMRP from infected Huh7 cells. RMRP was selected for several reasons: (1) RMRP interacts with approximately ten well-known proteins that serve as an internal control 15,23 ; (2) RMRP is not translated; and (3) RMRP does Adjusted P value CNBP NSP6 N S LARP4 STIP1 PUM1 YBX1 YBX3 NSP15 PABPC4 SYNCRIP G3BP2 YTHDF2 ORF3a RTCB PABPC1 SND1 M EIF4B UPF1 EIF4H MOV10 CSDE1 A1CF RBMS2 RAB6A RAB6D PPP1CC RPS2 SCFD1 NSP12 CAPRIN1 DDX3X EIF3E RPS14 NSP16 RPS10 RPL15 LSM14A HNRNPA1 IGF2BP2 LIN28B RYDEN STRAP NSP9 ACTR2 ANXA1 USO1 RPL6 CFL1 DDX1 HDLBP EIF5A PPP1CB RPL13 RPS3…”

A Novel Model for the RNase MRP-Induced Switch between the Formation of Different Forms of 5.8S rRNA

“…The results demonstrate that the 5.8S L processed from the ∆2 pre-rRNA is incorporated into 60S and 80S ribosomes as well as polysomes (Figure 8A, lanes 14-19 and lanes 21-27, respectively). Additionally, probing with O552 showed that the 5 -extended 5.8S RNA transcripts ("exoladders") were also incorporated into ribosomes, including polysomes (Figure 8A, lanes [42][43][44][45][46][47][48][49][50][51][52][53][54][55]. In other words, the extensions did not preclude incorporation of the 5.8S-containing rRNA into functional ribosomes.…”

“…It should be noted that, even though 8 nucleotides around the A3 consensus sequence contact the RNase MRP binding pocket, only two nucleotides in the consensus sequence have a strong effect on the rate of cleavage [46][47][48]. Thus, we cannot exclude ectopic RNase MRP cleavage of ∆14, ∆15, and ∆16 in the RRP2 strain, although if this were the case, we would have expected that such misplaced cleavage should also suppress the effect of the inhibition of A3 cleavage in the ∆18 mutant.…”

A Novel Model for the RNase MRP-Induced Switch Between Different Forms of 5.8S rRNA

“…It should be noted, however, that even though 8 nucleotides around the A3 consensus sequence contact the RNase MRP binding pocket, only two nucleotides in the consensus sequence have a strong effect on the rate of cleavage [38,39,41]. Thus, we cannot exclude ectopic RNase MRP cleavage of ∆14, ∆15, and ∆16 in the RRP2 strain, although if this were the case, we would have expected that such ectopic cleavage should also suppress the effect of the inhibition of A3 cleavage in the ∆18 mutant.…”