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A co-transcriptional ribosome assembly checkpoint controls nascent large ribosomal subunit maturation
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Abstract
During transcription of eukaryotic ribosomal DNA in the nucleolus, assembly checkpoints exist that guarantee the formation of stable precursors of small and large ribosomal subunits. While the formation of an early large subunit assembly checkpoint precedes the separation of small and large subunit maturation, its mechanism of action and function remain unknown. Here, we report the cryo-electron microscopy structure of the yeast co-transcriptional large ribosomal subunit assembly intermediate that serves as a checkpoint. The structure provides the mechanistic basis for how quality-control pathways are established through co-transcriptional ribosome assembly factors, that structurally interrogate, remodel and, together with ribosomal proteins, cooperatively stabilize correctly folded pre-ribosomal RNA. Our findings thus provide a molecular explanation for quality control during eukaryotic ribosome assembly in the nucleolus.
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Highly accurate protein structure prediction with AlphaFold
Jumper, J., Evans, R., Pritzel, A., Green, T., Figurnov, M., Ronneberger, O., Tunyasuvunakool, K., Bates, R., Žídek, A., Potapenko, A., et al. (2021) · Nature · doi:10.1038/s41586-021-03819-2 · Cited by 43,764
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Research works printed but not linked: 40
- Klinge, S. & Woolford, J. L. Ribosome assembly coming into focus. Nat. Rev. Mol. Cell Biol. 20, 116–131 (2019). · DOI
- Miller, O. L. & Beatty, B. R. Visualization of nucleolar genes. Science 164, 955–957 (1969). · DOI · Paper page
- Osheim, Y. N. et al. Pre-18S ribosomal RNA is structurally compacted into the SSU processome prior to being cleaved from nascent transcripts in Saccharomyces cerevisiae. Mol. Cell 16, 943–954 (2004). · DOI
- Hunziker, M. et al. Conformational switches control early maturation of the eukaryotic small ribosomal subunit. eLife 8, 213 (2019). · DOI
- Barandun, J., Hunziker, M. & Klinge, S. Assembly and structure of the SSU processome—a nucleolar precursor of the small ribosomal subunit. Curr. Opin. Struct. Biol. 49, 85–93 (2018). · DOI
- Eppens, N. A., Rensen, S., Granneman, S., Raué, H. A. & Venema, J. The roles of Rrp5p in the synthesis of yeast 18S and 5.8S rRNA can be functionally and physically separated. RNA 5, 779–793 (1999). · DOI
- Torchet, C., Jacq, C. & Hermann-Le Denmat, S. Two mutant forms of the S1/TPR-containing protein Rrp5p affect the 18S rRNA synthesis in Saccharomyces cerevisiae. RNA 4, 1636–1652 (1998). · DOI
- Venema, J. & Tollervey, D. RRP5 is required for formation of both 18S and 5.8S rRNA in yeast. EMBO J. 15, 5701–5714 (1996). · DOI
- Eppens, N. A. et al. Deletions in the S1 domain of Rrp5p cause processing at a novel site in ITS1 of yeast pre-rRNA that depends on Rex4p. Nucleic Acids Res. 30, 4222–4231 (2002). · DOI
- Lebaron, S. et al. Rrp5 binding at multiple sites coordinates pre-rRNA processing and assembly. Mol. Cell 52, 707–719 (2013). · DOI
- Hierlmeier, T. et al. Rrp5p, Noc1p and Noc2p form a protein module which is part of early large ribosomal subunit precursors in S. cerevisiae. Nucleic Acids Res. 40, 650–659 (2012). · DOI
- Chen, W., Xie, Z., Yang, F. & Ye, K. Stepwise assembly of the earliest precursors of large ribosomal subunits in yeast. Nucleic Acids Res. 45, 6837–6847 (2017). · DOI
- Chaker-Margot, M. & Klinge, S. Assembly and early maturation of large subunit precursors. RNA 25, rna.069799.118–471 (2019). · DOI
- Khoshnevis, S., Liu, X., Dattolo, M. D. & Karbstein, K. Rrp5 establishes a checkpoint for 60S assembly during 40S maturation. RNA 25, 1164–1176 (2019). · DOI
- Chaker-Margot, M., Hunziker, M., Barandun, J., Dill, B. D. & Klinge, S. Stage-specific assembly events of the 6-MDa small-subunit processome initiate eukaryotic ribosome biogenesis. Nat. Struct. Mol. Biol. 22, 920–923 (2015). · DOI
- Kater, L. et al. Visualizing the assembly pathway of nucleolar pre-60S ribosomes. Cell 171, 1599–1610 (2017). · DOI
- Zhou, D. et al. Cryo-EM structure of an early precursor of large ribosomal subunit reveals a half-assembled intermediate. Protein Cell 10, 120–130 (2018) · DOI
- Sanghai, Z. A. et al. Modular assembly of the nucleolar pre-60S ribosomal subunit. Nature 556, 126–129 (2018). · DOI
- Burlacu, E. et al. High-throughput RNA structure probing reveals critical folding events during early 60S ribosome assembly in yeast. Nat. Commun. 8, 714 (2017). · DOI
- Ben-Shem, A. et al. The structure of the eukaryotic ribosome at 3.0 Å resolution. Science 334, 1524–1529 (2011). · DOI
- Gamalinda, M. et al. A hierarchical model for assembly of eukaryotic 60S ribosomal subunit domains. Genes Dev. 28, 198–210 (2014). · DOI
- Milkereit, P. et al. Maturation and intranuclear transport of pre-ribosomes requires Noc proteins. Cell 105, 499–509 (2001). · DOI
- Sahasranaman, A. et al. Assembly of Saccharomyces cerevisiae 60S ribosomal subunits: role of factors required for 27S pre-rRNA processing. EMBO J. 30, 4020–4032 (2011). · DOI
- Ulirsch, J. C. et al. The genetic landscape of Diamond-Blackfan anemia. Am. J. Hum. Genet. 103, 930–947 (2018). · DOI · Paper page
- Vogel, N. et al. The landscape of pediatric Diamond-Blackfan anemia in Switzerland: genotype and phenotype characteristics. Eur. J. Pediatr. 180, 3581–3585 (2021). · DOI
- Destefanis, F. et al. Reduction of nucleolar NOC1 leads to the accumulation of pre-rRNAs and induces Xrp1, affecting growth and resulting in cell competition. J. Cell Sci. 135, jcs260110 (2022). · DOI
- Mastronarde, D. N. Automated electron microscope tomography using robust prediction of specimen movements. J. Struct. Biol. 152, 36–51 (2005). · DOI
- Rohou, A. & Grigorieff, N. CTFFIND4: fast and accurate defocus estimation from electron micrographs. J. Struct. Biol. 192, 216–221 (2015). · DOI
- Zivanov, J. et al. New tools for automated high-resolution cryo-EM structure determination in RELION-3. eLife 7, e42166 (2018). · DOI
- Wagner, T. et al. SPHIRE-crYOLO is a fast and accurate fully automated particle picker for cryo-EM. Commun. Biol. 2, 218–13 (2019). · DOI
- Cardone, G., Heymann, J. B. & Steven, A. C. One number does not fit all: mapping local variations in resolution in cryo-EM reconstructions. J. Struct. Biol. 184, 226–236 (2013). · DOI
- Punjani, A., Rubinstein, J. L., Fleet, D. J. & Brubaker, M. A. cryoSPARC: algorithms for rapid unsupervised cryo-EM structure determination. Nat. Methods 14, 290–296 (2017). · DOI · Paper page
- Adams, P. D. et al. PHENIX: a comprehensive Python-based system for macromolecular structure solution. Acta Crystallogr. D. Biol. Crystallogr. 66, 213–221 (2010). · DOI · Paper page
- Emsley, P. & Cowtan, K. Coot: model-building tools for molecular graphics. Acta Crystallogr. D. Biol. Crystallogr. 60, 2126–2132 (2004). · DOI · Paper page
- Pettersen, E. F. et al. UCSF ChimeraX: structure visualization for researchers, educators, and developers. Protein Sci. 30, 70–82 (2021). · DOI
- Rappsilber, J., Mann, M. & Ishihama, Y. Protocol for micro-purification, enrichment, pre-fractionation and storage of peptides for proteomics using StageTips. Nat. Protoc. 2, 1896–1906 (2007). · DOI · Paper page
- Cox, J. et al. Accurate proteome-wide label-free quantification by delayed normalization and maximal peptide ratio extraction, termed MaxLFQ. Mol. Cell Proteom. 13, 2513–2526 (2014). · DOI · Paper page
- Tyanova, S. et al. The Perseus computational platform for comprehensive analysis of (prote)omics data. Nat. Methods 13, 731–740 (2016). · DOI · Paper page
- Ashkenazy, H. et al. ConSurf 2016: an improved methodology to estimate and visualize evolutionary conservation in macromolecules. Nucleic Acids Res. 44, W344–W350 (2016). · DOI · Paper page
- Sievers, F. et al. Fast, scalable generation of high-quality protein multiple sequence alignments using Clustal Omega. Mol. Syst. Biol. 7, 539 (2011). · DOI
Metadata
- Authors
- Sanghai, Z. A., Piwowarczyk, R., Broeck, A. V., & Klinge, S.
- Affiliations
- Rockefeller University (US)
- Corresponding author
- Klinge, Sebastian
- Venue
- Nature Structural & Molecular Biology
- Published
- 2023-04-10
- Volume
- 30
- Issue
- 5
- Pages
- 594-599
- ISSN
- 1545-9985 (ISSN-L)
- 1545-9993
- PMC
- PMC10191850
- OpenAlex
- W4363673446
- Cited by
- 25
- References
- 1
- Citations by year
- 2026: 6 · 2025: 5 · 2024: 11 · 2023: 3
- FWCI
- 2.23
- Type
- journal article
- Language
- en
- Open access
- hybrid
- doi.org
- Locations
- Nature Structural & Molecular Biology (publishedVersion, cc-by)
- bioRxiv (Cold Spring Harbor Laboratory) (acceptedVersion)
- PubMed Central (publishedVersion, cc-by)
- PubMed (publishedVersion)
- ORBi (University of Liège) (submittedVersion, cc-by-nc-nd)
- Funders
- Leona M. and Harry B. Helmsley Charitable Trust
- G. Harold and Leila Y. Mathers Foundation
- National Institutes of Health
- National Institute of General Medical Sciences (R01GM143181)
- Topics
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › RNA and protein synthesis mechanisms
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Nuclear Structure and Function
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Genomics and Chromatin Dynamics
- Keywords
- ribosomal DNA transcription, nucleolus, quality control, yeast, ribosomal proteins
- MeSH terms
- Ribosomal Proteins, RNA, Ribosomal, Saccharomyces cerevisiae, Cryoelectron Microscopy, Saccharomyces cerevisiae Proteins, Ribosome Subunits, Large, Ribosome Subunits, Small, Eukaryotic, Ribosome Subunits, Large, Eukaryotic
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