Identification of Two Elusive Human Ribonuclease MRP-Specific Protein Components

Overview

Journal bioRxiv

Date 2025 Feb 3

PMID 39896489

Authors

Rui Che

Bhoomi Mirani

Monireh Panah

Xiaotong Chen

Hong Luo

Andrei Alexandrov

Affiliations

Soon will be listed here.

Abstract

All known protein components of one of the longest-studied human ribonucleoprotein ribozyme nuclear Ribonuclease MRP (RNase MRP), which processes pre-rRNA at ITS1 site 2, are shared with Ribonuclease P (RNase P), which cleaves pre-tRNA 5' leader sequences. Our genome-wide forward genetic screening identified two poorly characterized human genes, which we named RPP24 and RPP64. We show that these two genes are required for pre-rRNA ITS1 site 2 processing and their protein products efficiently associate with RNA MRP. Unlike all other human RNase MRP protein components, RPP24 and RPP64 are not required for RNase P activity and do not associate with RNase P-specific RNA H1. Despite extremely limited sequence homology, RPP24 and RPP64 exhibit predicted structural similarities to two RNase MRP-specific components in , with specific differences in RPP64 regions of substrate recognition. Collectively, our functional screening and validation revealed the first two protein components unique to human nuclear RNase MRP.

References

Hashimoto M, Sato T, Muroyama Y, Fujimura L, Hatano M, Saito T . Nepro is localized in the nucleolus and essential for preimplantation development in mice. Dev Growth Differ. 2015; 57(7):529-38. DOI: 10.1111/dgd.12232. View

Aulds J, Wierzbicki S, McNairn A, Schmitt M . Global identification of new substrates for the yeast endoribonuclease, RNase mitochondrial RNA processing (MRP). J Biol Chem. 2012; 287(44):37089-97. PMC: 3481309. DOI: 10.1074/jbc.M112.389023. View

Zhou B, Wan F, Lei K, Lan P, Wu J, Lei M . Coevolution of RNA and protein subunits in RNase P and RNase MRP, two RNA processing enzymes. J Biol Chem. 2024; 300(3):105729. PMC: 10966300. DOI: 10.1016/j.jbc.2024.105729. View

Piccinelli P, Alm Rosenblad M, Samuelsson T . Identification and analysis of ribonuclease P and MRP RNA in a broad range of eukaryotes. Nucleic Acids Res. 2005; 33(14):4485-95. PMC: 1183490. DOI: 10.1093/nar/gki756. View

Garcia P, Leach R, Wadsworth G, Choudhary K, Li H, Aviran S . Stability and nuclear localization of yeast telomerase depend on protein components of RNase P/MRP. Nat Commun. 2020; 11(1):2173. PMC: 7195438. DOI: 10.1038/s41467-020-15875-9. View

Lan P, Tan M, Zhang Y, Niu S, Chen J, Shi S . Structural insight into precursor tRNA processing by yeast ribonuclease P. Science. 2018; 362(6415). DOI: 10.1126/science.aat6678. View

Esakova O, Krasilnikov A . Of proteins and RNA: the RNase P/MRP family. RNA. 2010; 16(9):1725-47. PMC: 2924533. DOI: 10.1261/rna.2214510. View

Rambout X, Maquat L . Nuclear mRNA decay: regulatory networks that control gene expression. Nat Rev Genet. 2024; 25(10):679-697. PMC: 11408106. DOI: 10.1038/s41576-024-00712-2. View

Camacho C, Coulouris G, Avagyan V, Ma N, Papadopoulos J, Bealer K . BLAST+: architecture and applications. BMC Bioinformatics. 2009; 10:421. PMC: 2803857. DOI: 10.1186/1471-2105-10-421. View

10.

Belgrader P, Cheng J, Maquat L . Evidence to implicate translation by ribosomes in the mechanism by which nonsense codons reduce the nuclear level of human triosephosphate isomerase mRNA. Proc Natl Acad Sci U S A. 1993; 90(2):482-6. PMC: 45687. DOI: 10.1073/pnas.90.2.482. View

11.

Gardiner K, Marsh T, Pace N, Altman S . The RNA moiety of ribonuclease P is the catalytic subunit of the enzyme. Cell. 1983; 35(3 Pt 2):849-57. DOI: 10.1016/0092-8674(83)90117-4. View

12.

Wu J, Niu S, Tan M, Huang C, Li M, Song Y . Cryo-EM Structure of the Human Ribonuclease P Holoenzyme. Cell. 2018; 175(5):1393-1404.e11. DOI: 10.1016/j.cell.2018.10.003. View

13.

Cai T, Aulds J, Gill T, Cerio M, Schmitt M . The Saccharomyces cerevisiae RNase mitochondrial RNA processing is critical for cell cycle progression at the end of mitosis. Genetics. 2002; 161(3):1029-42. PMC: 1462176. DOI: 10.1093/genetics/161.3.1029. View

14.

Narayanan D, Shukla A, Kausthubham N, Bhavani G, Shah H, Mortier G . An emerging ribosomopathy affecting the skeleton due to biallelic variations in NEPRO. Am J Med Genet A. 2019; 179(9):1709-1717. DOI: 10.1002/ajmg.a.61267. View

15.

Shalem O, Sanjana N, Hartenian E, Shi X, Scott D, Mikkelson T . Genome-scale CRISPR-Cas9 knockout screening in human cells. Science. 2013; 343(6166):84-87. PMC: 4089965. DOI: 10.1126/science.1247005. View

16.

Chang D, Clayton D . A mammalian mitochondrial RNA processing activity contains nucleus-encoded RNA. Science. 1987; 235(4793):1178-84. DOI: 10.1126/science.2434997. View

17.

Skeparnias I, Bou-Nader C, Anastasakis D, Fan L, Wang Y, Hafner M . Structural basis of MALAT1 RNA maturation and mascRNA biogenesis. Nat Struct Mol Biol. 2024; 31(11):1655-1668. DOI: 10.1038/s41594-024-01340-4. View

18.

Sunwoo H, Dinger M, Wilusz J, Amaral P, Mattick J, Spector D . MEN epsilon/beta nuclear-retained non-coding RNAs are up-regulated upon muscle differentiation and are essential components of paraspeckles. Genome Res. 2008; 19(3):347-59. PMC: 2661813. DOI: 10.1101/gr.087775.108. View

19.

Lemieux B, Laterreur N, Perederina A, Noel J, Dubois M, Krasilnikov A . Active Yeast Telomerase Shares Subunits with Ribonucleoproteins RNase P and RNase MRP. Cell. 2016; 165(5):1171-1181. PMC: 4874874. DOI: 10.1016/j.cell.2016.04.018. View

20.

Altman S . The road to RNase P. Nat Struct Biol. 2000; 7(10):827-8. DOI: 10.1038/79566. View