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Plassart L, Shayan R, Montellese C, Rinaldi D, Larburu N, Pichereaux C, Froment C, Lebaron S, O'Donohue MF, Kutay U, Marcoux J, Gleizes PE, Plisson-Chastang C. The final step of 40S ribosomal subunit maturation is controlled by a dual key lock. eLife 2021; 10:61254. [PMID: 33908345 PMCID: PMC8112863 DOI: 10.7554/elife.61254] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/20/2020] [Accepted: 04/19/2021] [Indexed: 12/31/2022] Open
Abstract
Preventing premature interaction of pre-ribosomes with the translation apparatus is essential for translational accuracy. Hence, the final maturation step releasing functional 40S ribosomal subunits, namely processing of the 18S ribosomal RNA 3' end, is safeguarded by the protein DIM2, which both interacts with the endoribonuclease NOB1 and masks the rRNA cleavage site. To elucidate the control mechanism that unlocks NOB1 activity, we performed cryo-electron microscopy analysis of late human pre-40S particles purified using a catalytically inactive form of the ATPase RIO1. These structures, together with in vivo and in vitro functional analyses, support a model in which ATP-loaded RIO1 cooperates with ribosomal protein RPS26/eS26 to displace DIM2 from the 18S rRNA 3' end, thereby triggering final cleavage by NOB1; release of ADP then leads to RIO1 dissociation from the 40S subunit. This dual key lock mechanism requiring RIO1 and RPS26 guarantees the precise timing of pre-40S particle conversion into translation-competent ribosomal subunits.
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Affiliation(s)
- Laura Plassart
- Molecular, Cellular and Developmental Biology department (MCD), Centre de Biologie Integrative (CBI), University of Toulouse, CNRS, UPS, Toulouse, France
| | - Ramtin Shayan
- Molecular, Cellular and Developmental Biology department (MCD), Centre de Biologie Integrative (CBI), University of Toulouse, CNRS, UPS, Toulouse, France
| | | | - Dana Rinaldi
- Molecular, Cellular and Developmental Biology department (MCD), Centre de Biologie Integrative (CBI), University of Toulouse, CNRS, UPS, Toulouse, France
| | - Natacha Larburu
- Molecular, Cellular and Developmental Biology department (MCD), Centre de Biologie Integrative (CBI), University of Toulouse, CNRS, UPS, Toulouse, France
| | - Carole Pichereaux
- Institut de Pharmacologie et Biologie Structurale, Université de Toulouse, CNRS, UPS, Toulouse, France
| | - Carine Froment
- Institut de Pharmacologie et Biologie Structurale, Université de Toulouse, CNRS, UPS, Toulouse, France
| | - Simon Lebaron
- Molecular, Cellular and Developmental Biology department (MCD), Centre de Biologie Integrative (CBI), University of Toulouse, CNRS, UPS, Toulouse, France
| | - Marie-Françoise O'Donohue
- Molecular, Cellular and Developmental Biology department (MCD), Centre de Biologie Integrative (CBI), University of Toulouse, CNRS, UPS, Toulouse, France
| | - Ulrike Kutay
- Institut für Biochemie, ETH Zürich, Zurich, Switzerland
| | - Julien Marcoux
- Institut de Pharmacologie et Biologie Structurale, Université de Toulouse, CNRS, UPS, Toulouse, France
| | - Pierre-Emmanuel Gleizes
- Molecular, Cellular and Developmental Biology department (MCD), Centre de Biologie Integrative (CBI), University of Toulouse, CNRS, UPS, Toulouse, France
| | - Celia Plisson-Chastang
- Molecular, Cellular and Developmental Biology department (MCD), Centre de Biologie Integrative (CBI), University of Toulouse, CNRS, UPS, Toulouse, France
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Shayan R, Rinaldi D, Larburu N, Plassart L, Balor S, Bouyssié D, Lebaron S, Marcoux J, Gleizes PE, Plisson-Chastang C. Good Vibrations: Structural Remodeling of Maturing Yeast Pre-40S Ribosomal Particles Followed by Cryo-Electron Microscopy. Molecules 2020; 25:molecules25051125. [PMID: 32138239 PMCID: PMC7179242 DOI: 10.3390/molecules25051125] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/20/2020] [Revised: 02/24/2020] [Accepted: 02/27/2020] [Indexed: 12/03/2022] Open
Abstract
Assembly of eukaryotic ribosomal subunits is a very complex and sequential process that starts in the nucleolus and finishes in the cytoplasm with the formation of functional ribosomes. Over the past few years, characterization of the many molecular events underlying eukaryotic ribosome biogenesis has been drastically improved by the “resolution revolution” of cryo-electron microscopy (cryo-EM). However, if very early maturation events have been well characterized for both yeast ribosomal subunits, little is known regarding the final maturation steps occurring to the small (40S) ribosomal subunit. To try to bridge this gap, we have used proteomics together with cryo-EM and single particle analysis to characterize yeast pre-40S particles containing the ribosome biogenesis factor Tsr1. Our analyses lead us to refine the timing of the early pre-40S particle maturation steps. Furthermore, we suggest that after an early and structurally stable stage, the beak and platform domains of pre-40S particles enter a “vibrating” or “wriggling” stage, that might be involved in the final maturation of 18S rRNA as well as the fitting of late ribosomal proteins into their mature position.
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Affiliation(s)
- Ramtin Shayan
- Laboratoire de Biologie Moléculaire Eucaryote, Centre de Biologie Intégrative, Université de Toulouse, CNRS, UPS, 118 route de Narbonne, 31062 Toulouse CEDEX, France; (R.S.); (D.R.); (N.L.); (L.P.); (S.B.); (S.L.)
| | - Dana Rinaldi
- Laboratoire de Biologie Moléculaire Eucaryote, Centre de Biologie Intégrative, Université de Toulouse, CNRS, UPS, 118 route de Narbonne, 31062 Toulouse CEDEX, France; (R.S.); (D.R.); (N.L.); (L.P.); (S.B.); (S.L.)
| | - Natacha Larburu
- Laboratoire de Biologie Moléculaire Eucaryote, Centre de Biologie Intégrative, Université de Toulouse, CNRS, UPS, 118 route de Narbonne, 31062 Toulouse CEDEX, France; (R.S.); (D.R.); (N.L.); (L.P.); (S.B.); (S.L.)
| | - Laura Plassart
- Laboratoire de Biologie Moléculaire Eucaryote, Centre de Biologie Intégrative, Université de Toulouse, CNRS, UPS, 118 route de Narbonne, 31062 Toulouse CEDEX, France; (R.S.); (D.R.); (N.L.); (L.P.); (S.B.); (S.L.)
| | - Stéphanie Balor
- Laboratoire de Biologie Moléculaire Eucaryote, Centre de Biologie Intégrative, Université de Toulouse, CNRS, UPS, 118 route de Narbonne, 31062 Toulouse CEDEX, France; (R.S.); (D.R.); (N.L.); (L.P.); (S.B.); (S.L.)
| | - David Bouyssié
- Institut de Pharmacologie et Biologie Structurale, Université de Toulouse, CNRS, UPS, 205 route de Narbonne, 31062 Toulouse CEDEX, France;
| | - Simon Lebaron
- Laboratoire de Biologie Moléculaire Eucaryote, Centre de Biologie Intégrative, Université de Toulouse, CNRS, UPS, 118 route de Narbonne, 31062 Toulouse CEDEX, France; (R.S.); (D.R.); (N.L.); (L.P.); (S.B.); (S.L.)
| | - Julien Marcoux
- Laboratoire de Biologie Moléculaire Eucaryote, Centre de Biologie Intégrative, Université de Toulouse, CNRS, UPS, 118 route de Narbonne, 31062 Toulouse CEDEX, France; (R.S.); (D.R.); (N.L.); (L.P.); (S.B.); (S.L.)
- Correspondence: (J.M.); (P.-E.G.); (C.P.-C.)
| | - Pierre-Emmanuel Gleizes
- Laboratoire de Biologie Moléculaire Eucaryote, Centre de Biologie Intégrative, Université de Toulouse, CNRS, UPS, 118 route de Narbonne, 31062 Toulouse CEDEX, France; (R.S.); (D.R.); (N.L.); (L.P.); (S.B.); (S.L.)
- Correspondence: (J.M.); (P.-E.G.); (C.P.-C.)
| | - Célia Plisson-Chastang
- Laboratoire de Biologie Moléculaire Eucaryote, Centre de Biologie Intégrative, Université de Toulouse, CNRS, UPS, 118 route de Narbonne, 31062 Toulouse CEDEX, France; (R.S.); (D.R.); (N.L.); (L.P.); (S.B.); (S.L.)
- Correspondence: (J.M.); (P.-E.G.); (C.P.-C.)
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Mitterer V, Shayan R, Ferreira-Cerca S, Murat G, Enne T, Rinaldi D, Weigl S, Omanic H, Gleizes PE, Kressler D, Plisson-Chastang C, Pertschy B. Conformational proofreading of distant 40S ribosomal subunit maturation events by a long-range communication mechanism. Nat Commun 2019; 10:2754. [PMID: 31227701 PMCID: PMC6588571 DOI: 10.1038/s41467-019-10678-z] [Citation(s) in RCA: 31] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/05/2018] [Accepted: 05/23/2019] [Indexed: 12/21/2022] Open
Abstract
Eukaryotic ribosomes are synthesized in a hierarchical process driven by a plethora of assembly factors, but how maturation events at physically distant sites on pre-ribosomes are coordinated is poorly understood. Using functional analyses and cryo-EM, we show that ribosomal protein Rps20 orchestrates communication between two multi-step maturation events across the pre-40S subunit. Our study reveals that during pre-40S maturation, formation of essential contacts between Rps20 and Rps3 permits assembly factor Ltv1 to recruit the Hrr25 kinase, thereby promoting Ltv1 phosphorylation. In parallel, a deeply buried Rps20 loop reaches to the opposite pre-40S side, where it stimulates Rio2 ATPase activity. Both cascades converge to the final maturation steps releasing Rio2 and phosphorylated Ltv1. We propose that conformational proofreading exerted via Rps20 constitutes a checkpoint permitting assembly factor release and progression of pre-40S maturation only after completion of all earlier maturation steps. The biogenesis of eukaryotic ribosomes is a multi-step process involving the action of more than 200 different ribosome assembly factors. Here the authors show that Rps20 acts as a conduit to coordinate maturation steps across the head domain of the nascent small ribosomal subunit.
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Affiliation(s)
- Valentin Mitterer
- Institute for Molecular Biosciences, University of Graz, Humboldtstrasse 50, 8010, Graz, Austria.,Biochemistry Centre, University of Heidelberg, 69120, Heidelberg, Germany
| | - Ramtin Shayan
- Laboratoire de Biologie Moléculaire Eucaryote, Centre de Biologie Intégrative, Université de Toulouse, CNRS, UPS, 118 route de Narbonne, 31062, Toulouse Cedex, France
| | - Sébastien Ferreira-Cerca
- Biochemistry III - Institute for Biochemistry, Genetics and Microbiology, University of Regensburg, Universitätsstraße 31, 93053, Regensburg, Germany.
| | - Guillaume Murat
- Unit of Biochemistry, Department of Biology, University of Fribourg, Chemin du Musée 10, 1700, Fribourg, Switzerland
| | - Tanja Enne
- Institute for Molecular Biosciences, University of Graz, Humboldtstrasse 50, 8010, Graz, Austria
| | - Dana Rinaldi
- Laboratoire de Biologie Moléculaire Eucaryote, Centre de Biologie Intégrative, Université de Toulouse, CNRS, UPS, 118 route de Narbonne, 31062, Toulouse Cedex, France
| | - Sarah Weigl
- Institute for Molecular Biosciences, University of Graz, Humboldtstrasse 50, 8010, Graz, Austria
| | - Hajrija Omanic
- Institute for Molecular Biosciences, University of Graz, Humboldtstrasse 50, 8010, Graz, Austria
| | - Pierre-Emmanuel Gleizes
- Laboratoire de Biologie Moléculaire Eucaryote, Centre de Biologie Intégrative, Université de Toulouse, CNRS, UPS, 118 route de Narbonne, 31062, Toulouse Cedex, France
| | - Dieter Kressler
- Unit of Biochemistry, Department of Biology, University of Fribourg, Chemin du Musée 10, 1700, Fribourg, Switzerland.
| | - Celia Plisson-Chastang
- Laboratoire de Biologie Moléculaire Eucaryote, Centre de Biologie Intégrative, Université de Toulouse, CNRS, UPS, 118 route de Narbonne, 31062, Toulouse Cedex, France.
| | - Brigitte Pertschy
- Institute for Molecular Biosciences, University of Graz, Humboldtstrasse 50, 8010, Graz, Austria.
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Belhabich-Baumas K, Joret C, Jády BE, Plisson-Chastang C, Shayan R, Klopp C, Henras AK, Henry Y, Mougin A. The Rio1p ATPase hinders premature entry into translation of late pre-40S pre-ribosomal particles. Nucleic Acids Res 2017; 45:10824-10836. [PMID: 28977579 PMCID: PMC5737503 DOI: 10.1093/nar/gkx734] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/02/2017] [Accepted: 08/17/2017] [Indexed: 12/03/2022] Open
Abstract
Cytoplasmic maturation of precursors to the small ribosomal subunit in yeast requires the intervention of a dozen assembly factors (AFs), the precise roles of which remain elusive. One of these is Rio1p that seems to intervene at a late step of pre-40S particle maturation. We have investigated the role played by Rio1p in the dynamic association and dissociation of AFs with and from pre-40S particles. Our results indicate that Rio1p depletion leads to the stalling of at least 4 AFs (Nob1p, Tsr1p, Pno1p/Dim2p and Fap7p) in 80S-like particles. We conclude that Rio1p is important for the timely release of these factors from 80S-like particles. In addition, we present immunoprecipitation and electron microscopy evidence suggesting that when Rio1p is depleted, a subset of Nob1p-containing pre-40S particles associate with translating polysomes. Using Nob1p as bait, we purified pre-40S particles from cells lacking Rio1p and performed ribosome profiling experiments which suggest that immature 40S subunits can carry out translation elongation. We conclude that lack of Rio1p allows premature entry of pre-40S particles in the translation process and that the presence of Nob1p and of the 18S rRNA 3′ extension in the 20S pre-rRNA is not incompatible with translation elongation.
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Affiliation(s)
- Kamila Belhabich-Baumas
- Laboratoire de Biologie Moléculaire Eucaryote, Centre de Biologie Intégrative (CBI), Université de Toulouse, CNRS, UPS, 31000 Toulouse, France
| | - Clément Joret
- Laboratoire de Biologie Moléculaire Eucaryote, Centre de Biologie Intégrative (CBI), Université de Toulouse, CNRS, UPS, 31000 Toulouse, France
| | - Beáta E Jády
- Laboratoire de Biologie Moléculaire Eucaryote, Centre de Biologie Intégrative (CBI), Université de Toulouse, CNRS, UPS, 31000 Toulouse, France
| | - Célia Plisson-Chastang
- Laboratoire de Biologie Moléculaire Eucaryote, Centre de Biologie Intégrative (CBI), Université de Toulouse, CNRS, UPS, 31000 Toulouse, France
| | - Ramtin Shayan
- Laboratoire de Biologie Moléculaire Eucaryote, Centre de Biologie Intégrative (CBI), Université de Toulouse, CNRS, UPS, 31000 Toulouse, France
| | - Christophe Klopp
- Unité de Mathématiques et Informatique Appliquées, INRA, 31320 Castanet Tolosan, France
| | - Anthony K Henras
- Laboratoire de Biologie Moléculaire Eucaryote, Centre de Biologie Intégrative (CBI), Université de Toulouse, CNRS, UPS, 31000 Toulouse, France
| | - Yves Henry
- Laboratoire de Biologie Moléculaire Eucaryote, Centre de Biologie Intégrative (CBI), Université de Toulouse, CNRS, UPS, 31000 Toulouse, France
| | - Annie Mougin
- Laboratoire de Biologie Moléculaire Eucaryote, Centre de Biologie Intégrative (CBI), Université de Toulouse, CNRS, UPS, 31000 Toulouse, France
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Shukla L, Taylor G, Shayan R. The pedicled inferior paraumbilical perforator (I-PUP) flap for a volar wrist defect: A reconstructive solution across the ages. J Plast Reconstr Aesthet Surg 2013; 66:1613-5. [DOI: 10.1016/j.bjps.2013.02.011] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/10/2012] [Revised: 12/29/2012] [Accepted: 02/14/2013] [Indexed: 11/30/2022]
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Syme D, Shayan R, Grinsell D. Muscle-only intra-oral mucosal defect reconstruction. J Plast Reconstr Aesthet Surg 2012; 65:1654-9. [DOI: 10.1016/j.bjps.2012.06.006] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/28/2011] [Revised: 05/22/2012] [Accepted: 06/10/2012] [Indexed: 12/01/2022]
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Shayan R, Syme D, Grinsell D. The IMAP flap for pharygoesophageal reconstruction following stricture release. J Plast Reconstr Aesthet Surg 2012; 65:810-3. [DOI: 10.1016/j.bjps.2011.11.016] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/18/2011] [Accepted: 11/07/2011] [Indexed: 11/26/2022]
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Shayan R, Karnesis T, Achen MG, Mann GB, Stacker SA, Taylor GI. SO05 THE NATURE OF NEARBY LYMPHATICS DICTATES WHETHER A VASCULAR ENDOTHELIAL GROWTH FACTOR-D (VEGF-D) INDUCES TUMOR LYMPHATICS AND METASTASIS. ANZ J Surg 2007. [DOI: 10.1111/j.1445-2197.2007.04131_5.x] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
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Shayan R, Karnesis T, Paavonen K, Achen MG, Taylor GI, Stacker SA. PR07 A SYSTEM FOR QUANTIFYING LYMPHATIC VESSEL ABNORMALITIES IN LYMPHEDEMA MODELS, AND LOCO-SYSTEMIC EFFECTS OF PRO-LYMPHATIC TUMOR GROWTH FACTORS. ANZ J Surg 2007. [DOI: 10.1111/j.1445-2197.2007.04127_7.x] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
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Kaplan ED, Rozen WM, Shayan R, Bernard S, Taylor GI, Ashton MW. PR05 POST-OPERATIVE HAEMATOMAS IN MICROVASCULAR FREE FLAP RECONSTRUCTION OF THE HEAD AND NECK: THE INCIDENCE, AETIOLOGY AND OUTCOME MODIFICATIONS. ANZ J Surg 2007. [DOI: 10.1111/j.1445-2197.2007.04127_5.x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
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