In the past 25 years, genetic and biochemical analyses of ribosome assembly in yeast have identified most of the factors that participate in this complex pathway and have generated models for the mechanisms driving the assembly. More recently, the publication of numerous cryo-electron microscopy structures of yeast ribosome assembly intermediates has provided near-atomic resolution snapshots of ribosome precursor particles. Satisfyingly, these structural data support the genetic and biochemical models and provide additional mechanistic insight into ribosome assembly. In this Review, we discuss the mechanisms of assembly of the yeast small ribosomal subunit and large ribosomal subunit in the nucleolus, nucleus and cytoplasm. Particular emphasis is placed on concepts such as the mechanisms of RNA compaction, the functions of molecular switches and molecular mimicry, the irreversibility of assembly checkpoints and the roles of structural and functional proofreading of pre-ribosomal particles.
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de la Cruz, J., Karbstein, K. & Woolford, J. L. Functions of ribosomal proteins in assembly of eukaryotic ribosomes in vivo. Annu. Rev. Biochem. 84, 93–129 (2015).
Rabl, J., Leibundgut, M., Ataide, S. F., Haag, A. & Ban, N. Crystal structure of the eukaryotic 40S ribosomal subunit in complex with initiation factor 1. Science 331, 730–736 (2011).
Klinge, S., Voigts-Hoffmann, F., Leibundgut, M., Arpagaus, S. & Ban, N. Crystal structure of the eukaryotic 60S ribosomal subunit in complex with initiation factor 6. Science 334, 941–948 (2011).
Ben-Shem, A. et al. The structure of the eukaryotic ribosome at 3.0 Å resolution. Science 334, 1524–1529 (2011).
Klinge, S., Voigts-Hoffmann, F., Leibundgut, M. & Ban, N. Atomic structures of the eukaryotic ribosome. Trends Biochem. Sci. 37, 189–198 (2012).
Melnikov, S. et al. One core, two shells: bacterial and eukaryotic ribosomes. Nat. Struct. Mol. Biol. 19, 560–567 (2012).
de la Cruz, J. et al. Feedback regulation of ribosome assembly. Curr. Genet. 64, 393–404 (2018).
Woolford, J. L. & Baserga, S. J. Ribosome biogenesis in the yeast Saccharomyces cerevisiae. Genetics 195, 643–681 (2013).
Engel, C., Sainsbury, S., Cheung, A. C., Kostrewa, D. & Cramer, P. RNA polymerase I structure and transcription regulation. Nature 502, 650–655 (2013).
Fernández-Tornero, C. et al. Crystal structure of the 14-subunit RNA polymerase I. Nature 502, 644–649 (2013).
Engel, C., Plitzko, J. & Cramer, P. RNA polymerase I-Rrn3 complex at 4.8 Å resolution. Nat. Commun. 7, 12129 (2016).
Tafur, L. et al. Molecular structures of transcribing RNA polymerase I. Mol. Cell 64, 1135–1143 (2016).
Neyer, S. et al. Structure of RNA polymerase I transcribing ribosomal DNA genes. Nature 540, 607–610 (2016).
Engel, C. et al. Structural basis of RNA polymerase I transcription initiation. Cell 169, 120–131 (2017).
Nogi, Y., Yano, R. & Nomura, M. Synthesis of large rRNAs by RNA polymerase II in mutants of Saccharomyces cerevisiae defective in RNA polymerase I. Proc. Natl Acad. Sci. USA 88, 3962–3966 (1991).
Torreira, E. et al. The dynamic assembly of distinct RNA polymerase I complexes modulates rDNA transcription. eLife 6, e20832 (2017).
Fernández-Pevida, A., Kressler, D. & de la Cruz, J. Processing of preribosomal RNA in Saccharomyces cerevisiae. WIREs RNA 6, 191–209 (2015).
Udem, S. A. & Warner, J. R. Ribosomal RNA synthesis in Saccharomyces cerevisiae. J. Mol. Biol. 65, 227–242 (1972).
Trapman, J., Retèl, J. & Planta, R. J. Ribosomal precursor particles from yeast. Exp. Cell Res. 90, 95–104 (1975).
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).
Kos, M. & Tollervey, D. Yeast pre-rRNA processing and modification occur cotranscriptionally. Mol. Cell 37, 809–820 (2010).
Sharma, S. & Lafontaine, D. L. J. ‘View from a bridge’: a new perspective on eukaryotic rRNA base modification. Trends Biochem. Sci. 40, 560–575 (2015).
Kiss, T., Fayet-Lebaron, E. & Jády, B. E. Box H/ACA small ribonucleoproteins. Mol. Cell 37, 597–606 (2010).
Watkins, N. J. & Bohnsack, M. T. The box C/D and H/ACA snoRNPs: key players in the modification, processing and the dynamic folding of ribosomal RNA. Wiley Interdiscip. Rev. RNA 3, 397–414 (2011).
Henry, Y. et al. The 5ʹ end of yeast 5.8S rRNA is generated by exonucleases from an upstream cleavage site. EMBO J. 13, 2452–2463 (1994).
Lygerou, Z., Allmang, C., Tollervey, D. & Séraphin, B. Accurate processing of a eukaryotic precursor ribosomal RNA by ribonuclease MRP in vitro. Science 272, 268–270 (1996).
Martin, R., Straub, A. U., Doebele, C. & Bohnsack, M. T. DExD/H-box RNA helicases in ribosome biogenesis. RNA Biol. 10, 4–18 (2013).
Rodríguez-Galán, O., García-Gómez, J. J. & de la Cruz, J. Yeast and human RNA helicases involved in ribosome biogenesis: current status and perspectives. Biochim. Biophys. Acta 1829, 775–790 (2013).
Kressler, D., Hurt, E., Bergler, H. & Bassler, J. The power of AAA-ATPases on the road of pre-60S ribosome maturation — molecular machines that strip pre-ribosomal particles. Biochim. Biophys. Acta 1823, 92–100 (2011).
Pillet, B., Mitterer, V., Kressler, D. & Pertschy, B. Hold on to your friends: dedicated chaperones of ribosomal proteins: dedicated chaperones mediate the safe transfer of ribosomal proteins to their site of pre-ribosome incorporation. BioEssays 39, 1–12 (2017).
Peña, C., Hurt, E. & Panse, V. G. Eukaryotic ribosome assembly, transport and quality control. Nat. Struct. Mol. Biol. 24, 689–699 (2017).
Miller, O. L. & Beatty, B. R. Visualization of nucleolar genes. Science 164, 955–957 (1969).
Mougey, E. B. et al. The terminal balls characteristic of eukaryotic rRNA transcription units in chromatin spreads are rRNA processing complexes. Genes Dev. 7, 1609–1619 (1993).
Mougey, E. B., Pape, L. K. & Sollner-Webb, B. A. U3 small nuclear ribonucleoprotein-requiring processing event in the 5' external transcribed spacer of Xenopus precursor rRNA. Mol. Cell. Biol. 13, 5990–5998 (1993).
Dragon, F. et al. A large nucleolar U3 ribonucleoprotein required for 18S ribosomal RNA biogenesis. Nature 417, 967–970 (2002).
Grandi, P. et al. 90S pre-ribosomes include the 35S pre-rRNA, the U3 snoRNP, and 40S subunit processing factors but predominantly lack 60S synthesis factors. Mol. Cell 10, 105–115 (2002).
Kornprobst, M. et al. Architecture of the 90S pre-ribosome: a structural view on the birth of the eukaryotic ribosome. Cell 166, 380–393 (2016).
Chaker-Margot, M., Barandun, J., Hunziker, M. & Klinge, S. Architecture of the yeast small subunit processome. Science 355, eaal1880 (2017).
Sun, Q. et al. Molecular architecture of the 90S small subunit pre-ribosome. eLife 6, e22086 (2017).
Rorbach, J., Aibara, S. & Amunts, A. Ribosome origami. Nat. Struct. Mol. Biol. 24, 879–881 (2017).
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).
Zhang, L., Wu, C., Cai, G., Chen, S. & Ye, K. Stepwise and dynamic assembly of the earliest precursors of small ribosomal subunits in yeast. Genes Dev. 30, 718–732 (2016).
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). References 41–43 describe ribosome assembly as a function of transcription using truncated rRNA mimics.
Krogan, N. J. et al. High-definition macromolecular composition of yeast RNA-processing complexes. Mol. Cell 13, 225–239 (2004).
Dosil, M. & Bustelo, X. R. Functional characterization of Pwp2, a WD family protein essential for the assembly of the 90S pre-ribosomal particle. J. Biol. Chem. 279, 37385–37397 (2004).
Pöll, G. et al. In vitro reconstitution of yeast tUTP/UTP A and UTP B subcomplexes provides new insights into their modular architecture. PLOS ONE 9, e114898 (2014).
Hunziker, M. et al. UtpA and UtpB chaperone nascent pre-ribosomal RNA and U3 snoRNA to initiate eukaryotic ribosome assembly. Nat. Commun. 7, 12090 (2016).
Pérez-Fernández, J., Román, A., De Las Rivas, J., Bustelo, X. R. & Dosil, M. The 90S preribosome is a multimodular structure that is assembled through a hierarchical mechanism. Mol. Cell. Biol. 27, 5414–5429 (2007).
Pérez-Fernández, J., Martín-Marcos, P. & Dosil, M. Elucidation of the assembly events required for the recruitment of Utp20, Imp4 and Bms1 onto nascent pre-ribosomes. Nucleic Acids Res. 39, 8105–8121 (2011).
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).
Beltrame, M. & Tollervey, D. Identification and functional analysis of two U3 binding sites on yeast pre-ribosomal. RNA 11, 1531–1542 (1992).
Beltrame, M., Henry, Y. & Tollervey, D. Mutational analysis of an essential binding site for the U3 snoRNA in the 5ʹ external transcribed spacer of yeast pre-rRNA. Nucleic Acids Res. 22, 4057–4065 (1994).
Marmier-Gourrier, N., Cléry, A., Schlotter, F., Senty-Ségault, V. & Branlant, C. A second base pair interaction between U3 small nucleolar RNA and the 5ʹ-ETS region is required for early cleavage of the yeast pre-ribosomal RNA. Nucleic Acids Res. 39, 9731–9745 (2011).
Dutca, L. M., Gallagher, J. E. G. & Baserga, S. J. The initial U3 snoRNA: pre-rRNA base pairing interaction required for pre-18S rRNA folding revealed by in vivo chemical probing. Nucleic Acids Res. 39, 5164–5180 (2011).
Puchta, O. et al. Network of epistatic interactions within a yeast snoRNA. Science 352, 840–844 (2016).
Cheng, J., Kellner, N., Berninghausen, O., Hurt, E. & Beckmann, R. 3.2-Å-resolution structure of the 90S preribosome before A1 pre-rRNA cleavage. Nat. Struct. Mol. Biol. 24, 954–964 (2017).
Barandun, J. et al. The complete structure of the small-subunit processome. Nat. Struct. Mol. Biol. 24, 944–953 (2017). References 56 and 57 describe the structure of the SSU processome at near-atomic resolution.
Sá-Moura, B. et al. Mpp10 represents a platform for the interaction of multiple factors within the 90S pre-ribosome. PLOS ONE 12, e0183272 (2017).
Koš, M. & Tollervey, D. The putative RNA helicase Dbp4p is required for release of the U14 snoRNA from preribosomes in Saccharomyces cerevisiae. Mol. Cell 20, 53–64 (2005).
Martin, R. et al. A pre-ribosomal RNA interaction network involving snoRNAs and the Rok1 helicase. RNA 20, 1173–1182 (2014).
Wells, G. R. et al. The ribosome biogenesis factor yUtp23/hUTP23 coordinates key interactions in the yeast and human pre-40S particle and hUTP23 contains an essential PIN domain. Nucleic Acids Res. 45, 4796–4809 (2017).
Soltanieh, S., Lapensée, M. & Dragon, F. Nucleolar proteins Bfr2 and Enp2 interact with DEAD-box RNA helicase Dbp4 in two different complexes. Nucleic Acids Res. 42, 3194–3206 (2014).
Shu, S. & Ye, K. Structural and functional analysis of ribosome assembly factor Efg1. Nucleic Acids Res. 46, 2096–2106 (2018).
Segerstolpe, A., Lundkvist, P., Osheim, Y. N., Beyer, A. L. & Wieslander, L. Mrd1p binds to pre-rRNA early during transcription independent of U3 snoRNA and is required for compaction of the pre-rRNA into small subunit processomes. Nucleic Acids Res. 36, 4364–4380 (2008).
Wery, M., Ruidant, S., Schillewaert, S., Leporé, N. & Lafontaine, D. L. J. The nuclear poly(A) polymerase and exosome cofactor Trf5 is recruited cotranscriptionally to nucleolar surveillance. RNA 15, 406–419 (2009).
Gamalinda, M. et al. A hierarchical model for assembly of eukaryotic 60S ribosomal subunit domains. Genes Dev. 28, 198–210 (2014).
Wells, G. R. et al. The PIN domain endonuclease Utp24 cleaves pre-ribosomal RNA at two coupled sites in yeast and humans. Nucleic Acids Res. 44, 5399–5409 (2016).
Tomecki, R., Labno, A., Drazkowska, K., Cysewski, D. & Dziembowski, A. hUTP24 is essential for processing of the human rRNA precursor at site A1, but not at site A0. RNA Biol. 12, 1010–1029 (2015).
Calviño, F. R. et al. Structural basis for 5ʹ-ETS recognition by Utp4 at the early stages of ribosome biogenesis. PLOS ONE 12, e0178752 (2017).
Zhang, C. et al. Integrative structural analysis of the UTPB complex, an early assembly factor for eukaryotic small ribosomal subunits. Nucleic Acids Res. 44, 7475–7486 (2016).
Zhang, C. et al. Structure of Utp21 tandem WD domain provides insight into the organization of the UTPB complex involved in ribosome synthesis. PLOS ONE 9, e86540 (2014).
Boissier, F., Schmidt, C. M., Linnemann, J., Fribourg, S. & Perez-Fernandez, J. Pwp2 mediates UTP-B assembly via two structurally independent domains. Sci. Rep. 7, 3169 (2017).
Zhang, L., Lin, J. & Ye, K. Structural and functional analysis of the U3 snoRNA binding protein Rrp9. RNA 19, 701–711 (2013).
Delprato, A. et al. Crucial role of the Rcl1p-Bms1p interaction for yeast pre-ribosomal RNA processing. Nucleic Acids Res. 42, 10161–10172 (2014).
Thomas, S. R., Keller, C. A., Szyk, A., Cannon, J. R. & LaRonde-LeBlanc, N. A. Structural insight into the functional mechanism of Nep1/Emg1 N1-specific pseudouridine methyltransferase in ribosome biogenesis. Nucleic Acids Res. 39, 2445–2457 (2011).
Zheng, S., Lan, P., Liu, X. & Ye, K. Interaction between ribosome assembly factors Krr1 and Faf1 is essential for formation of small ribosomal subunit in yeast. J. Biol. Chem. 289, 22692–22703 (2014).
Lin, J., Lu, J., Feng, Y., Sun, M. & Ye, K. An RNA-binding complex involved in ribosome biogenesis contains a protein with homology to tRNA CCA-adding enzyme. PLOS Biol. 11, e1001669 (2013).
Lim, Y. H., Charette, J. M. & Baserga, S. J. Assembling a protein-protein interaction map of the SSU processome from existing datasets. PLOS ONE 6, e17701 (2011).
Bassler, J. et al. Interaction network of the ribosome assembly machinery from a eukaryotic thermophile. Protein Sci. 26, 327–342 (2017).
Vincent, N. G., Charette, J. M. & Baserga, S. J. The SSU processome interactome in Saccharomyces cerevisiae reveals novel protein subcomplexes. RNA 24, 77–89 (2018).
Sharma, S. et al. Yeast Kre33 and human NAT10 are conserved 18S rRNA cytosine acetyltransferases that modify tRNAs assisted by the adaptor Tan1/THUMPD1. Nucleic Acids Res. 43, 2242–2258 (2015).
Wegierski, T., Billy, E., Nasr, F. & Filipowicz, W. Bms1p, a G-domain-containing protein, associates with Rcl1p and is required for 18S rRNA biogenesis in yeast. RNA 7, 1254–1267 (2001).
Gelperin, D., Horton, L., Beckman, J., Hensold, J. & Lemmon, S. K. Bms1p, a novel GTP-binding protein, and the related Tsr1p are required for distinct steps of 40S ribosome biogenesis in yeast. RNA 7, 1268–1283 (2001).
Sardana, R. et al. The DEAH-box helicase Dhr1 dissociates U3 from the pre-rRNA to promote formation of the central pseudoknot. PLOS Biol. 13, e1002083 (2015).
Zhu, J., Liu, X., Anjos, M., Correll, C. C. & Johnson, A. W. Utp14 recruits and activates the RNA helicase Dhr1 to undock U3 snoRNA from the pre-ribosome. Mol. Cell. Biol. 36, 965–978 (2016).
Thoms, M. et al. The exosome is recruited to RNA substrates through specific adaptor proteins. Cell 162, 1029–1038 (2015).
Mitchell, P. Rrp47 and the function of the Sas10/C1D domain. Biochem. Soc. Trans. 38, 1088–1092 (2010).
Venema, J. & Tollervey, D. RRP5 is required for formation of both 18S and 5.8S rRNA in yeast. EMBO J. 15, 5701–5714 (1996).
Milkereit, P. et al. Maturation and intranuclear transport of pre-ribosomes requires Noc proteins. Cell 105, 499–509 (2001).
Young, C. L. & Karbstein, K. The roles of S1 RNA-binding domains in Rrp5’s interactions with pre-rRNA. RNA 17, 512–521 (2011).
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).
Lebaron, S. et al. Rrp5 binding at multiple sites coordinates pre-rRNA processing and assembly. Mol. Cell 52, 707–719 (2013).
Sun, C. & Woolford, J. L. The yeast NOP4 gene product is an essential nucleolar protein required for pre-rRNA processing and accumulation of 60S ribosomal subunits. EMBO J. 13, 3127–3135 (1994).
Bergès, T., Petfalski, E., Tollervey, D. & Hurt, E. C. Synthetic lethality with fibrillarin identifies NOP77p, a nucleolar protein required for pre-rRNA processing and modification. EMBO J. 13, 3136–3148 (1994).
Granneman, S., Petfalski, E. & Tollervey, D. A cluster of ribosome synthesis factors regulate pre-rRNA folding and 5.8S rRNA maturation by the Rat1 exonuclease. 30, 4006–4019 (2011).
Dez, C. et al. Npa1p, a component of very early pre-60S ribosomal particles, associates with a subset of small nucleolar RNPs required for peptidyl transferase center modification. Mol. Cell. Biol. 24, 6324–6337 (2004).
Rosado, I. V. et al. Characterization of Saccharomyces cerevisiae Npa2p (Urb2p) reveals a low-molecular-mass complex containing Dbp6p, Npa1p (Urb1p), Nop8p, and Rsa3p involved in early steps of 60S ribosomal subunit biogenesis. Mol. Cell. Biol. 27, 1207–1221 (2007).
Joret, C. et al. The Npa1p complex chaperones the assembly of the earliest eukaryotic large ribosomal subunit precursor. PLOS Genet. 14, e1007597 (2018).
Sloan, K. E. & Bohnsack, M. T. Unravelling the mechanisms of RNA helicase regulation. Trends Biochem. Sci. 43, 237–250 (2018).
Turowski, T. W. & Tollervey, D. Cotranscriptional events in eukaryotic ribosome synthesis. Wiley Interdiscip. Rev. RNA 6, 129–139 (2015).
Allmang, C. & Tollervey, D. The role of the 3ʹ external transcribed spacer in yeast pre-rRNA processing. J. Mol. Biol. 278, 67–78 (1998).
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).
Sanghai, Z. A. et al. Modular assembly of the nucleolar pre-60S ribosomal subunit. Nature 556, 126–129 (2018).
Kater, L. et al. Visualizing the assembly pathway of nucleolar pre-60S ribosomes. Cell 171, 1599–1610 (2017).
Zhou, D. et al. Cryo-EM structure of an early precursor of large ribosomal subunit reveals a half-assembled intermediate. Protein Cell https://doi.org/10.1007/s13238-018-0526-7 (2018). References 103–105 describe the structures of nucleolar pre-60S precursors.
Kressler, D., Roser, D., Pertschy, B. & Hurt, E. The AAA ATPase Rix7 powers progression of ribosome biogenesis by stripping Nsa1 from pre-60S particles. J. Cell Biol. 181, 935–944 (2008).
Bradatsch, B. et al. Structure of the pre-60S ribosomal subunit with nuclear export factor Arx1 bound at the exit tunnel. Nat. Struct. Mol. Biol. 19, 1234–1241 (2012).
Wu, S. et al. Diverse roles of assembly factors revealed by structures of late nuclear pre-60S ribosomes. Nature 534, 133–137 (2016). This paper describes the high-resolution structure of the late nucleolar Nog2 particle.
Biedka, S. et al. Hierarchical recruitment of ribosomal proteins and assembly factors remodels nucleolar pre-60S ribosomes. J. Cell Biol. 217, 2503–2518 (2018).
Zhang, J. et al. Assembly factors Rpf2 and Rrs1 recruit 5S rRNA and ribosomal proteins rpL5 and rpL11 into nascent ribosomes. Genes Dev. 21, 2580–2592 (2007).
Kressler, D. et al. Synchronizing nuclear import of ribosomal proteins with ribosome assembly. Science 338, 666–671 (2012).
Calviño, F. R. et al. Symportin 1 chaperones 5S RNP assembly during ribosome biogenesis by occupying an essential rRNA-binding site. Nat. Commun. 6, 6510 (2015).
Talkish, J., Zhang, J., Jakovljevic, J., Horsey, E. W. & Woolford, J. L. Hierarchical recruitment into nascent ribosomes of assembly factors required for 27SB pre-rRNA processing in Saccharomyces cerevisiae. Nucleic Acids Res. 40, 8646–8661 (2012).
Bassler, J. et al. The AAA-ATPase Rea1 drives removal of biogenesis factors during multiple stages of 60S ribosome assembly. Mol. Cell 38, 712–721 (2010).
Wegrecki, M., Rodríguez-Galán, O., de la Cruz, J. & Bravo, J. The structure of Erb1-Ytm1 complex reveals the functional importance of a high-affinity binding between two β-propellers during the assembly of large ribosomal subunits in eukaryotes. Nucleic Acids Res. 43, 11017–11030 (2015).
Romes, E. M., Sobhany, M. & Stanley, R. E. The crystal structure of the ubiquitin-like domain of ribosome assembly factor Ytm1 and characterization of its interaction with the AAA-ATPase Midasin. J. Biol. Chem. 291, 882–893 (2016).
Thoms, M., Ahmed, Y. L., Maddi, K., Hurt, E. & Sinning, I. Concerted removal of the Erb1–Ytm1 complex in ribosome biogenesis relies on an elaborate interface. Nucleic Acids Res. 44, 926–939 (2016).
Konikkat, S., Biedka, S. & Woolford, J. L. The assembly factor Erb1 functions in multiple remodeling events during 60S ribosomal subunit assembly in S. cerevisiae. Nucleic Acids Res. 45, 4853–4865 (2017).
Barrio-Garcia, C. et al. Architecture of the Rix1-Rea1 checkpoint machinery during pre-60S-ribosome remodeling. Nat. Struct. Mol. Biol. 23, 37–44 (2016). This paper describes the architecture of the nuclear pre-60S particle containing the AAA-ATPase midasin.
Mitchell, P., Petfalski, E., Shevchenko, A., Mann, M. & Tollervey, D. The exosome: a conserved eukaryotic RNA processing complex containing multiple 3ʹ→5ʹ exoribonucleases. Cell 91, 457–466 (1997).
Falk, S. et al. Structural insights into the interaction of the nuclear exosome helicase Mtr4 with the preribosomal protein Nop53. RNA 23, 1780–1787 (2017).
Rodríguez-Galán, O., García-Gómez, J. J., Kressler, D. & de la Cruz, J. Immature large ribosomal subunits containing the 7S pre-rRNA can engage in translation in Saccharomyces cerevisiae. RNA Biol. 12, 838–846 (2015).
Sarkar, A. et al. Preribosomes escaping from the nucleus are caught during translation by cytoplasmic quality control. Nat. Struct. Mol. Biol. 24, 1107–1115 (2017).
Allmang, C., Mitchell, P., Petfalski, E. & Tollervey, D. Degradation of ribosomal RNA precursors by the exosome. Nucleic Acids Res. 28, 1684–1691 (2000).
Castle, C. D. et al. Las1 interacts with Grc3 polynucleotide kinase and is required for ribosome synthesis in Saccharomyces cerevisiae. Nucleic Acids Res. 41, 1135–1150 (2013).
Pillon, M. C., Sobhany, M., Borgnia, M. J., Williams, J. G. & Stanley, R. E. Grc3 programs the essential endoribonuclease Las1 for specific RNA cleavage. Proc. Natl Acad. Sci. USA 114, E5530–E5538 (2017).
Gasse, L., Flemming, D. & Hurt, E. Coordinated ribosomal ITS2 RNA processing by the Las1 complex integrating endonuclease, polynucleotide kinase, and exonuclease activities. Mol. Cell 60, 808–815 (2015).
Schillewaert, S., Wacheul, L., Lhomme, F. & Lafontaine, D. L. J. The evolutionarily conserved protein Las1 is required for pre-rRNA processing at both ends of ITS2. Mol. Cell. Biol. 32, 430–444 (2012).
Fromm, L. et al. Reconstitution of the complete pathway of ITS2 processing at the pre-ribosome. Nat. Commun. 8, 1787 (2017).
Schuller, J. M., Falk, S., Fromm, L., Hurt, E. & Conti, E. Structure of the nuclear exosome captured on a maturing preribosome. Science 360, 219–222 (2018).
Thomson, E. & Tollervey, D. The final step in 5.8S rRNA processing is cytoplasmic in Saccharomyces cerevisiae. Mol. Cell. Biol. 30, 976–984 (2010).
Leidig, C. et al. 60S ribosome biogenesis requires rotation of the 5S ribonucleoprotein particle. Nat. Commun. 5, 3491 (2014).
Kharde, S., Calviño, F. R., Gumiero, A., Wild, K. & Sinning, I. The structure of Rpf2-Rrs1 explains its role in ribosome biogenesis. Nucleic Acids Res. 43, 7083–7095 (2015).
Madru, C. et al. Chaperoning 5S RNA assembly. Genes Dev. 29, 1432–1446 (2015).
Asano, N. et al. Structural and functional analysis of the Rpf2–Rrs1 complex in ribosome biogenesis. Nucleic Acids Res. 43, 4746–4757 (2015).
Karbstein, K. Quality control mechanisms during ribosome maturation. Trends Cell Biol. 23, 242–250 (2013).
Greber, B. J., 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. 19, 1228–1233 (2012).
Peisker, K. et al. Ribosome-associated complex binds to ribosomes in close proximity of Rpl31 at the exit of the polypeptide tunnel in yeast. Mol. Biol. Cell 19, 5279–5288 (2008).
Kramer, G., Boehringer, D., Ban, N. & Bukau, B. The ribosome as a platform for co-translational processing, folding and targeting of newly synthesized proteins. Nat. Struct. Mol. Biol. 16, 589–597 (2009).
Matsuo, Y. et al. Coupled GTPase and remodelling ATPase activities form a checkpoint for ribosome export. Nature 505, 112–116 (2014).
Manikas, R.-G., Thomson, E., Thoms, M. & Hurt, E. The K+-dependent GTPase Nug1 is implicated in the association of the helicase Dbp10 to the immature peptidyl transferase centre during ribosome maturation. Nucleic Acids Res. 44, 1800–1812 (2016).
Ma, C. et al. Structural snapshot of cytoplasmic pre-60S ribosomal particles bound by Nmd3, Lsg1, Tif6 and Reh1. Nat. Struct. Mol. Biol. 24, 214–220 (2017).
Malyutin, A. G., Musalgaonkar, S., Patchett, S., Frank, J. & Johnson, A. W. Nmd3 is a structural mimic of eIF5A, and activates the cpGTPase Lsg1 during 60S ribosome biogenesis. EMBO J. 36, 854–868 (2017). References 137, 142 and 143 describe the structures of cytoplasmic precursors of the large ribosomal subunit.
Sarkar, A., Pech, M., Thoms, M., Beckmann, R. & Hurt, E. Ribosome-stalk biogenesis is coupled with recruitment of nuclear-export factor to the nascent 60S subunit. Nat. Struct. Mol. Biol. 23, 1074–1082 (2016).
Rodnina, M. V., Fischer, N., Maracci, C. & Stark, H. Ribosome dynamics during decoding. Phil. Trans. R. Soc. B, Biol. Sci. 372, 20160182 (2017).
Panse, V. G. & Johnson, A. W. Maturation of eukaryotic ribosomes: acquisition of functionality. Trends Biochem. Sci. 35, 260–266 (2010).
Lo, K.-Y. et al. Defining the pathway of cytoplasmic maturation of the 60S ribosomal subunit. Mol. Cell 39, 196–208 (2010).
Pertschy, B. et al. Cytoplasmic recycling of 60S preribosomal factors depends on the AAA protein Drg1. Mol. Cell. Biol. 27, 6581–6592 (2007).
Kappel, L. et al. Rlp24 activates the AAA-ATPase Drg1 to initiate cytoplasmic pre-60S maturation. J. Cell Biol. 199, 771–782 (2012).
Altvater, M. et al. Targeted proteomics reveals compositional dynamics of 60S pre-ribosomes after nuclear export. Mol. Syst. Biol. 8, 628 (2012).
Hung, N.-J. & Johnson, A. W. Nuclear recycling of the pre-60S ribosomal subunit-associated factor Arx1 depends on Rei1 in Saccharomyces cerevisiae. Mol. Cell. Biol. 26, 3718–3727 (2006).
Lebreton, A. A functional network involved in the recycling of nucleocytoplasmic pre-60S factors. J. Cell Biol. 173, 349–360 (2006).
Meyer, A. E., Hoover, L. A. & Craig, E. A. The cytosolic J-protein, Jjj1, and Rei1 function in the removal of the pre-60S subunit factor Arx1. J. Biol. Chem. 285, 961–968 (2010).
Greber, B. J. et al. Insertion of the biogenesis factor Rei1 probes the ribosomal tunnel during 60S maturation. Cell 164, 91–102 (2016).
Bussiere, C., Hashem, Y., Arora, S., Frank, J. & Johnson, A. W. Integrity of the P-site is probed during maturation of the 60S ribosomal subunit. J. Cell Biol. 197, 747–759 (2012). References 147 and 155 describe functional proofreading of the large ribosomal subunit precursors.
Weis, F. et al. Mechanism of eIF6 release from the nascent 60S ribosomal subunit. Nat. Struct. Mol. Biol. 22, 914–919 (2015).
Heuer, A. et al. Cryo-EM structure of a late pre-40S ribosomal subunit from Saccharomyces cerevisiae. eLife 6, e30189 (2017).
Scaiola, A. et al. Structure of a eukaryotic cytoplasmic pre-40S ribosomal subunit. EMBO J. 37, e98499 (2018). References 157 and 158 describe the structure of the late cytoplasmic pre-40S particle.
Moriggi, G., Nieto, B. & Dosil, M. Rrp12 and the Exportin Crm1 participate in late assembly events in the nucleolus during 40S ribosomal subunit biogenesis. PLOS Genet. 10, e1004836 (2014).
Johnson, M. C., Ghalei, H., Doxtader, K. A., Karbstein, K. & Stroupe, M. E. Structural heterogeneity in pre-40S ribosomes. Structure 25, 329–340 (2017).
McCaughan, U. M. et al. Pre-40S ribosome biogenesis factor Tsr1 is an inactive structural mimic of translational GTPases. Nat. Commun. 7, 11789 (2016).
Schütz, S. et al. A RanGTP-independent mechanism allows ribosomal protein nuclear import for ribosome assembly. eLife 3, e03473 (2014).
Ferreira-Cerca, S., Kiburu, I., Thomson, E., LaRonde, N. & Hurt, E. Dominant Rio1 kinase/ATPase catalytic mutant induces trapping of late pre-40S biogenesis factors in 80S-like ribosomes. Nucleic Acids Res. 42, 8635–8647 (2014).
Turowski, T. W. et al. Rio1 mediates ATP-dependent final maturation of 40S ribosomal subunits. Nucleic Acids Res. 42, 12189–12199 (2014).
Lebaron, S. et al. Proofreading of pre-40S ribosome maturation by a translation initiation factor and 60S subunits. Nat. Struct. Mol. Biol. 19, 744–753 (2012).
Strunk, B. S., Novak, M. N., Young, C. L. & Karbstein, K. A translation-like cycle is a quality control checkpoint for maturing 40S ribosome subunits. Cell 150, 111–121 (2012). References 165 and 166 illustrate how functional proofreading of the small ribosomal subunit is carried out in the cytoplasm.
Ghalei, H. et al. The ATPase Fap7 tests the ability to carry out translocation-like conformational changes and releases Dim1 during 40S ribosome maturation. Mol. Cell 67, 990–1000 (2017).
Henras, A. K., Plisson-Chastang, C., O’Donohue, M.-F., Chakraborty, A. & Gleizes, P.-E. An overview of pre-ribosomal RNA processing in eukaryotes. Wiley Interdiscip. Rev. RNA 6, 225–242 (2015).
Wild, T. et al. A protein inventory of human ribosome biogenesis reveals an essential function of exportin 5 in 60S subunit export. PLOS Biol. 8, e1000522 (2010).
Tafforeau, L. et al. The complexity of human ribosome biogenesis revealed by systematic nucleolar screening of pre-rRNA processing factors. Mol. Cell 51, 539–551 (2013).
Badertscher, L. et al. Genome-wide RNAi screening identifies protein modules required for 40S subunit synthesis in human cells. Cell Rep. 13, 2879–2891 (2015).
Nicolas, E. et al. Involvement of human ribosomal proteins in nucleolar structure and p53-dependent nucleolar stress. Nat. Commun. 7, 11390 (2016).
Farley-Barnes, K. I. et al. Diverse regulators of human ribosome biogenesis discovered by changes in nucleolar number. Cell Rep. 22, 1923–1934 (2018).
Sulima, S. O., Hofman, I. J. F., De Keersmaecker, K. & Dinman, J. D. How ribosomes translate cancer. Cancer Discov. 7, 1069–1087 (2017).
Narla, A. & Ebert, B. L. Ribosomopathies: human disorders of ribosome dysfunction. Blood 115, 3196–3205 (2010).
Farley, K. I. & Baserga, S. J. Probing the mechanisms underlying human diseases in making ribosomes. Biochem. Soc. Trans. 44, 1035–1044 (2016).
Draptchinskaia, N. et al. The gene encoding ribosomal protein S19 is mutated in Diamond-Blackfan anaemia. Nat. Genet. 21, 169–175 (1999).
Choesmel, V. et al. Impaired ribosome biogenesis in Diamond-Blackfan anemia. Blood 109, 1275–1283 (2007).
Bolze, A. et al. Ribosomal protein SA haploinsufficiency in humans with isolated congenital asplenia. Science 340, 976–978 (2013).
Chagnon, P. et al. A missense mutation (R565W) in cirhin (FLJ14728) in North American Indian childhood cirrhosis. Am. J. Hum. Genet. 71, 1443–1449 (2002).
Ebert, B. L. et al. Identification of RPS14 as a 5q- syndrome gene by RNA interference screen. Nature 451, 335–339 (2008).
Trainor, P. A., Dixon, J. & Dixon, M. J. Treacher Collins syndrome: etiology, pathogenesis and prevention. Eur. J. Hum. Genet. 17, 275–283 (2009).
Warren, A. J. Molecular basis of the human ribosomopathy Shwachman–Diamond syndrome. Adv. Biol. Regul. 67, 109–127 (2018).
Mills, E. W. & Green, R. Ribosomopathies: there’s strength in numbers. Science 358, eaan2755 (2017).
Marechal, V., Elenbaas, B., Piette, J., Nicolas, J. C. & Levine, A. J. The ribosomal L5 protein is associated with mdm-2 and mdm-2–p53 complexes. Mol. Cell. Biol. 14, 7414–7420 (1994).
Bursac´, S. et al. Mutual protection of ribosomal proteins L5 and L11 from degradation is essential for p53 activation upon ribosomal biogenesis stress. Proc. Natl Acad. Sci. USA 109, 20467–20472 (2012).
Sloan, K. E., Bohnsack, M. T. & Watkins, N. J. The 5S RNP couples p53 homeostasis to ribosome biogenesis and nucleolar stress. Cell Rep. 5, 237–247 (2013).
Jaako, P. et al. Disruption of the 5S RNP-Mdm2 interaction significantly improves the erythroid defect in a mouse model for Diamond–Blackfan anemia. Leukemia 29, 2221–2229 (2015).
Jones, N. C. et al. Prevention of the neurocristopathy Treacher Collins syndrome through inhibition of p53 function. Nat. Med. 14, 125–133 (2008).
Barlow, J. L. et al. A p53-dependent mechanism underlies macrocytic anemia in a mouse model of human 5q– syndrome. Nat. Med. 16, 59–66 (2010).
Wilkins, B. J., Lorent, K., Matthews, R. P. & Pack, M. p53-mediated biliary defects caused by knockdown of cirh1a, the zebrafish homolog of the gene responsible for North American Indian childhood cirrhosis. PLOS ONE 8, e77670 (2013).
O’Donohue, M.-F., Choesmel, V., Faubladier, M., Fichant, G. & Gleizes, P.-E. Functional dichotomy of ribosomal proteins during the synthesis of mammalian 40S ribosomal subunits. J. Cell Biol. 190, 853–866 (2010).
Boria, I. et al. The ribosomal basis of Diamond–Blackfan anemia: mutation and database update. Hum. Mutat. 31, 1269–1279 (2010).
Gripp, K. W. et al. Diamond-Blackfan anemia with mandibulofacial dystostosis is heterogeneous, including the novel DBA genes TSR2 and RPS28. Am. J. Med. Genet. A 164A, 2240–2249 (2014).
Xue, S. & Barna, M. Specialized ribosomes: a new frontier in gene regulation and organismal biology. Nat. Rev. Mol. Cell. Biol. 13, 355–369 (2012).
Sankaran, V. G. et al. Exome sequencing identifies GATA1 mutations resulting in Diamond–Blackfan anemia. J. Clin. Invest. 122, 2439–2443 (2012).
Ludwig, L. S. et al. Altered translation of GATA1 in Diamond–Blackfan anemia. Nat. Med. 20, 748–753 (2014).
Khajuria, R. K. et al. Ribosome levels selectively regulate translation and lineage commitment in human hematopoiesis. Cell 173, 90–103 (2018). This paper shows that limiting ribosome levels causes defects in lineage commitment in patients with DBA.
Wu, S., Tan, D., Woolford, J. L., Dong, M.-Q. & Gao, N. Atomic modeling of the ITS2 ribosome assembly subcomplex from cryo-EM together with mass spectrometry-identified protein-protein crosslinks. Protein Sci. 26, 103–112 (2017).
Loibl, M. et al. The drug diazaborine blocks ribosome biogenesis by inhibiting the AAA-ATPase Drg1. J. Biol. Chem. 289, 3913–3922 (2014).
Zisser, G. et al. Viewing pre-60S maturation at a minute’s timescale. Nucleic Acids Res. 46, 3140–3151 (2018).
Kawashima, S. A. et al. Potent, reversible, and specific chemical inhibitors of eukaryotic ribosome biogenesis. Cell 167, 512–524 (2016). References 200–202 show the use of small-molecule inhibitors to block specific stages of eukaryotic ribosome assembly.
Talkish, J. et al. Disruption of ribosome assembly in yeast blocks cotranscriptional pre-rRNA processing and affects the global hierarchy of ribosome biogenesis. RNA 22, 852–866 (2016).
Albert, B. et al. A molecular titration system coordinates ribosomal protein gene transcription with ribosomal RNA synthesis. Mol. Cell 64, 720–733 (2016).
Prouteau, M. et al. TORC1 organized in inhibited domains (TOROIDs) regulate TORC1 activity. Nature 550, 265–269 (2017).
Shen, K. et al. Architecture of the human GATOR1 and GATOR1-Rag GTPases complexes. Nature 556, 64–69 (2018).
Mangan, H., Gailín, M. Ó. & McStay, B. Integrating the genomic architecture of human nucleolar organizer regions with the biophysical properties of nucleoli. FEBS J. 284, 3977–3985 (2017).
The authors thank members of the Woolford laboratory for comments on the manuscript and members of the Klinge laboratory for help with Fig. 2. The authors apologize to those whose work could not be discussed owing to space limitations.
Nature Reviews Molecular Cell Biology thanks A. Johnson and D. Lafontaine for their contribution to the peer review of this work.
The authors declare no competing interests.
Springer Nature remains neutral with regard to jurisdictional claims in published maps and institutional affiliations.
- Ribosomal proteins
Seventy-nine protein components of mature ribosomal subunits in yeast. Most are essential for assembly of their respective subunits.
- Decoding site
The functional centre of the small subunit, where the anticodon of an amino-acyl tRNA undergoes base pairing with the respective codon in the mRNA.
- Peptidyl transferase centre
(PTC). The active site of the large subunit, located in its interface, where ribosomal RNA catalyses the formation of peptide bonds and the hydrolysis of peptidyl-tRNA bonds.
- Central pseudoknot
An architectural motif within the small ribosomal subunit ribosomal RNA, at the interface of the four subdomains of the small ribosomal subunit.
- Central protuberance
A module that includes the 5S ribonucleoprotein and helices 80 and 82–88 of 25S ribosomal RNA, located at the top of the mature large ribosomal subunit.
- GTPase activating centre
(GAC). Within mature, large ribosomal subunits, the site that binds to and activates GTPases that participate in translation initiation and elongation.
- P0 stalk
A complex of three ribosomal proteins bound to helices 43 and 44 in 25S ribosomal RNA, which forms a stalk structure in mature large ribosomal subunits, to which translation factors bind.
- Polypeptide exit tunnel
(PET). A tunnel through which nascent polypeptides traverse the large ribosomal subunit. It comprises mostly ribosomal RNA and extends from the peptidyl transferase centre to the solvent side of the large subunit.
- Small nucleolar ribonucleoproteins
(snoRNPs). Complexes of small nucleolar RNAs (snoRNAs) and proteins. Base pairing of specific snoRNAs with target sequences in ribosomal RNA (rRNA) directs either methylation or pseudouridylation of the rRNA.
- Assembly factors
Proteins or protein complexes with roles in ribosome assembly. Most are present in ribosome assembly intermediates but none are components of mature ribosomes.
- Molecular mimicry
Refers to the activity of proteins for which the structure mimics that of other proteins (or of RNA). In ribosome assembly, molecular mimicry is used to block distinct sites by steric hindrance and prevent early binding of a structurally related protein.
- Molecular switches
Refers to factors that can switch between two states (for example, an assembly factor present or absent in a pre-ribosome) in response to internal hardwiring or an external cue.
- External and internal transcribed spacers
RNA sequences in the primary ribosomal RNA (rRNA) transcript, which are removed during ribosome biogenesis by a series of endonucleolytic or exonucleolytic reactions. They are thought to aid in proper folding of nascent rRNA.
- 90S particles
The very early pre-ribosomal particles containing the 35S pre-ribosomal RNA, which includes transcripts for both small and large ribosomal subunits.
- Miller spreads
Visualization of actively transcribed chromatin by electron microscopy of fixed, gently lysed nuclei, first used to look at transcription of ribosomal DNA repeats in Xenopus laevis.
(ATPases associated with diverse cellular activities). There are three different AAA-ATPases that function as ribosome assembly factors to remove other assembly factors from pre-ribosomes.
RNA oligonucleotides that are able to adopt a distinct shape and bind to a specific target with high specificity and affinity.
- Multimodal binding
Binding of a single protein to multiple ligands through separate binding sites in the protein.
A protein complex with 3ʹ to 5ʹ exonuclease activity, which processes cleaved pre-ribosomal RNA spacer sequences as well as other RNA species.
- Subunit interface
The surfaces of the small and large ribosomal subunits that face each other in functioning ribosomes.
- Ribosome quality control complex
A complex that extracts nascent polypeptides from ribosomes that have stalled in translation.
- E site
The specific binding site in ribosomes from which the deacylated (empty) tRNA exits from the ribosomes.
- P site
The specific binding site in ribosomes for peptidyl-tRNA.
- A site
The specific binding site in ribosomes for acceptor aminoacylated tRNA.
- Beak structure
A structure in the small ribosomal subunit consisting of a protrusion of helix 33 of the 18S ribosomal bound by ribosomal proteins.
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Klinge, S., Woolford, J.L. Ribosome assembly coming into focus. Nat Rev Mol Cell Biol 20, 116–131 (2019). https://doi.org/10.1038/s41580-018-0078-y
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