Structural Snapshots of Human Pre-60S Ribosomal Particles Before and After Nuclear Export

Overview

Journal Nat Commun

Specialty Biology

Date 2020 Jul 17

PMID 32669547

Citations 35

Authors

Xiaomeng Liang

Mei-Qing Zuo

Yunyang Zhang

Ningning Li

Chengying Ma

Meng-Qiu Dong

Ning Gao

Affiliations

Soon will be listed here.

Abstract

Ribosome biogenesis is an elaborate and energetically expensive program that involve two hundred protein factors in eukaryotes. Nuclear export of pre-ribosomal particles is one central step which also serves as an internal structural checkpoint to ensure the proper completion of nuclear assembly events. Here we present four structures of human pre-60S particles isolated through a nuclear export factor NMD3, representing assembly stages immediately before and after nuclear export. These structures reveal locations of a dozen of human factors, including an uncharacterized factor TMA16 localized between the 5S RNA and the P0 stalk. Comparison of these structures shows a progressive maturation for the functional regions, such as peptidyl transferase centre and peptide exit tunnel, and illustrate a sequence of factor-assisted rRNA maturation events. These data facilitate our understanding of the global conservation of ribosome assembly in eukaryotes and species-specific features of human assembly factors.

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References

Bassler J, Hurt E . Eukaryotic Ribosome Assembly. Annu Rev Biochem. 2018; 88:281-306. DOI: 10.1146/annurev-biochem-013118-110817. View

McCann K, Charette J, Vincent N, Baserga S . A protein interaction map of the LSU processome. Genes Dev. 2015; 29(8):862-75. PMC: 4403261. DOI: 10.1101/gad.256370.114. View

Ho C, Li X, Lai M, Terwilliger T, Beck J, Wohlschlegel J . Bottom-up structural proteomics: cryoEM of protein complexes enriched from the cellular milieu. Nat Methods. 2019; 17(1):79-85. PMC: 7494424. DOI: 10.1038/s41592-019-0637-y. View

Kraushar M, Krupp F, Harnett D, Turko P, Ambrozkiewicz M, Sprink T . Protein Synthesis in the Developing Neocortex at Near-Atomic Resolution Reveals Ebp1-Mediated Neuronal Proteostasis at the 60S Tunnel Exit. Mol Cell. 2020; 81(2):304-322.e16. PMC: 8163098. DOI: 10.1016/j.molcel.2020.11.037. View

Zhou Y, Musalgaonkar S, Johnson A, Taylor D . Tightly-orchestrated rearrangements govern catalytic center assembly of the ribosome. Nat Commun. 2019; 10(1):958. PMC: 6393466. DOI: 10.1038/s41467-019-08880-0. View

Pena C, Hurt E, Panse V . Eukaryotic ribosome assembly, transport and quality control. Nat Struct Mol Biol. 2017; 24(9):689-699. DOI: 10.1038/nsmb.3454. View

Chen Z, Meng J, Cao Y, Yin J, Fang R, Fan S . A high-speed search engine pLink 2 with systematic evaluation for proteome-scale identification of cross-linked peptides. Nat Commun. 2019; 10(1):3404. PMC: 6667459. DOI: 10.1038/s41467-019-11337-z. View

Greber B, Boehringer D, Montellese C, Ban N . Cryo-EM structures of Arx1 and maturation factors Rei1 and Jjj1 bound to the 60S ribosomal subunit. Nat Struct Mol Biol. 2012; 19(12):1228-33. DOI: 10.1038/nsmb.2425. View

Mills E, Green R . Ribosomopathies: There's strength in numbers. Science. 2017; 358(6363). DOI: 10.1126/science.aan2755. View

10.

Ma C, Wu S, Li N, Chen Y, Yan K, Li Z . Structural snapshot of cytoplasmic pre-60S ribosomal particles bound by Nmd3, Lsg1, Tif6 and Reh1. Nat Struct Mol Biol. 2017; 24(3):214-220. PMC: 5555584. DOI: 10.1038/nsmb.3364. View

11.

Williams C, Headd J, Moriarty N, Prisant M, Videau L, Deis L . MolProbity: More and better reference data for improved all-atom structure validation. Protein Sci. 2017; 27(1):293-315. PMC: 5734394. DOI: 10.1002/pro.3330. View

12.

Kirli K, Karaca S, Dehne H, Samwer M, Pan K, Lenz C . A deep proteomics perspective on CRM1-mediated nuclear export and nucleocytoplasmic partitioning. Elife. 2015; 4. PMC: 4764573. DOI: 10.7554/eLife.11466. View

13.

Klingauf-Nerurkar P, Gillet L, Portugal-Calisto D, Oborska-Oplova M, Jager M, Schubert O . The GTPase Nog1 co-ordinates the assembly, maturation and quality control of distant ribosomal functional centers. Elife. 2020; 9. PMC: 6968927. DOI: 10.7554/eLife.52474. View

14.

Bradatsch B, Leidig C, Granneman S, Gnadig M, Tollervey D, Bottcher B . Structure of the pre-60S ribosomal subunit with nuclear export factor Arx1 bound at the exit tunnel. Nat Struct Mol Biol. 2012; 19(12):1234-41. PMC: 3678077. DOI: 10.1038/nsmb.2438. View

15.

Larburu N, Montellese C, ODonohue M, Kutay U, Gleizes P, Plisson-Chastang C . Structure of a human pre-40S particle points to a role for RACK1 in the final steps of 18S rRNA processing. Nucleic Acids Res. 2016; 44(17):8465-78. PMC: 5041492. DOI: 10.1093/nar/gkw714. View

16.

Trotta C, Lund E, Kahan L, Johnson A, Dahlberg J . Coordinated nuclear export of 60S ribosomal subunits and NMD3 in vertebrates. EMBO J. 2003; 22(11):2841-51. PMC: 156746. DOI: 10.1093/emboj/cdg249. View

17.

Wong C, Traynor D, Basse N, Kay R, Warren A . Defective ribosome assembly in Shwachman-Diamond syndrome. Blood. 2011; 118(16):4305-12. DOI: 10.1182/blood-2011-06-353938. View

18.

Bohnsack K, Bohnsack M . Uncovering the assembly pathway of human ribosomes and its emerging links to disease. EMBO J. 2019; 38(13):e100278. PMC: 6600647. DOI: 10.15252/embj.2018100278. View

19.

Stelter P, Huber F, Kunze R, Flemming D, Hoelz A, Hurt E . Coordinated Ribosomal L4 Protein Assembly into the Pre-Ribosome Is Regulated by Its Eukaryote-Specific Extension. Mol Cell. 2015; 58(5):854-62. PMC: 6742479. DOI: 10.1016/j.molcel.2015.03.029. View

20.

Karbstein K . Quality control mechanisms during ribosome maturation. Trends Cell Biol. 2013; 23(5):242-50. PMC: 3640646. DOI: 10.1016/j.tcb.2013.01.004. View