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1. The final step of 40S ribosomal subunit maturation is controlled by a dual key lock

Author

Laura Plassart, Ramtin Shayan, Christian Montellese, Dana Rinaldi, Natacha Larburu, Carole Pichereaux, Carine Froment, Simon Lebaron, Marie-Françoise O'Donohue, Ulrike Kutay, Julien Marcoux, Pierre-Emmanuel Gleizes, and Celia Plisson-Chastang

Subjects
human ribosome biogenesis, small ribosomal subunit, structure-function study, cryo-EM, pre-rRNA processing, Medicine, Science, Biology (General), QH301-705.5
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.

Published
2021
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2. Good Vibrations: Structural Remodeling of Maturing Yeast Pre-40S Ribosomal Particles Followed by Cryo-Electron Microscopy

Author

Ramtin Shayan, Dana Rinaldi, Natacha Larburu, Laura Plassart, Stéphanie Balor, David Bouyssié, Simon Lebaron, Julien Marcoux, Pierre-Emmanuel Gleizes, and Célia Plisson-Chastang

Subjects
ribosome assembly, small ribosomal subunit, bottom-up proteomics, cryo-em, single particle analysis, Organic chemistry, QD241-441
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.

Published
2020
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3. Deciphering cellular and molecular determinants of human DPCD protein in complex with RUVBL1/RUVBL2 AAA-ATPases

Author

Raphael Dos Santos Morais, Paulo E. Santo, Marie Ley, Cédric Schelcher, Yoann Abel, Laura Plassart, Evolène Deslignière, Marie-Eve Chagot, Marc Quinternet, Ana C.F. Paiva, Steve Hessmann, Nelly Morellet, Pedro M. F. Sousa, Franck Vandermoere, Edouard Bertrand, Bruno Charpentier, Tiago M. Bandeiras, Célia Plisson-Chastang, Céline Verheggen, Sarah Cianférani, Xavier Manival, Ingénierie Moléculaire et Physiopathologie Articulaire (IMoPA), Université de Lorraine (UL)-Centre National de la Recherche Scientifique (CNRS), Instituto de Biologia Experimental e Tecnológica (IBET), Instituto de Tecnologia Química e Biológica António Xavier (ITQB), Universidade Nova de Lisboa = NOVA University Lisbon (NOVA), Laboratoire de Spectrométrie de Masse BioOrganique [Strasbourg] (LSMBO), Département Sciences Analytiques et Interactions Ioniques et Biomoléculaires (DSA-IPHC), Institut Pluridisciplinaire Hubert Curien (IPHC), Université de Strasbourg (UNISTRA)-Institut National de Physique Nucléaire et de Physique des Particules du CNRS (IN2P3)-Centre National de la Recherche Scientifique (CNRS)-Université de Strasbourg (UNISTRA)-Institut National de Physique Nucléaire et de Physique des Particules du CNRS (IN2P3)-Centre National de la Recherche Scientifique (CNRS)-Institut Pluridisciplinaire Hubert Curien (IPHC), Université de Strasbourg (UNISTRA)-Institut National de Physique Nucléaire et de Physique des Particules du CNRS (IN2P3)-Centre National de la Recherche Scientifique (CNRS)-Université de Strasbourg (UNISTRA)-Institut National de Physique Nucléaire et de Physique des Particules du CNRS (IN2P3)-Centre National de la Recherche Scientifique (CNRS), Infrastructure Nationale de Protéomique, FR2048 ProFI, Institut de génétique humaine (IGH), Centre National de la Recherche Scientifique (CNRS)-Université de Montpellier (UM), Unité de biologie moléculaire, cellulaire et du développement (MCD), Université Toulouse III - Paul Sabatier (UT3), Université Fédérale Toulouse Midi-Pyrénées-Université Fédérale Toulouse Midi-Pyrénées-Centre National de la Recherche Scientifique (CNRS)-Centre de Biologie Intégrative (CBI), Université Fédérale Toulouse Midi-Pyrénées-Université Fédérale Toulouse Midi-Pyrénées-Centre National de la Recherche Scientifique (CNRS)-Centre National de la Recherche Scientifique (CNRS), Ingénierie, Biologie et Santé en Lorraine (IBSLor), Institut National de la Santé et de la Recherche Médicale (INSERM)-Université de Lorraine (UL)-Centre National de la Recherche Scientifique (CNRS), Institut de Chimie des Substances Naturelles (ICSN), Institut de Chimie du CNRS (INC)-Université Paris-Saclay-Centre National de la Recherche Scientifique (CNRS), Institut de Génomique Fonctionnelle (IGF), Institut National de la Santé et de la Recherche Médicale (INSERM)-Centre National de la Recherche Scientifique (CNRS)-Université de Montpellier (UM), Université de Strasbourg (UNISTRA)-Institut National de Physique Nucléaire et de Physique des Particules du CNRS (IN2P3)-Centre National de la Recherche Scientifique (CNRS), Centre de Biologie Intégrative (CBI), Université Fédérale Toulouse Midi-Pyrénées-Université Fédérale Toulouse Midi-Pyrénées-Centre National de la Recherche Scientifique (CNRS), ANR-16-CE11-0032,snoRNPASSEMBLY,Comprendre l'assemblage des complexes macro-moléculaires en utilisant les snoRNP C/D comme modèle(2016), CIANFERANI, Sarah, and Comprendre l'assemblage des complexes macro-moléculaires en utilisant les snoRNP C/D comme modèle - - snoRNPASSEMBLY2016 - ANR-16-CE11-0032 - AAPG2016 - VALID

Subjects
[SDV]Life Sciences [q-bio], [SDV.BC]Life Sciences [q-bio]/Cellular Biology, Saxs, Structural Biology, Em, [CHIM] Chemical Sciences, [SDV.BBM] Life Sciences [q-bio]/Biochemistry, Molecular Biology, Humans, [CHIM]Chemical Sciences, [SDV.BBM]Life Sciences [q-bio]/Biochemistry, Molecular Biology, Lumier-IP, Molecular Biology, [SDV.BC] Life Sciences [q-bio]/Cellular Biology, XL-MS, Dpcd, DNA Helicases, Proteins, structural MS, Itc, Nmr, [SDV] Life Sciences [q-bio], Ruvbl1, Ruvbl2, Multiprotein Complexes, Silac-IP, ATPases Associated with Diverse Cellular Activities, Carrier Proteins
Abstract

International audience; DPCD is a protein that may play a role in cilia formation and whose absence leads to primary ciliary dyskinesia (PCD), a rare disease caused by impairment of ciliated cells. Except for high-throughput studies that identified DPCD as a possible RUVBL1 (R1) and RUVBL2 (R2) partner, no in-depth cellular, biochemical, and structural investigation involving DPCD have been reported so far. R1 and R2 proteins are ubiquitous highly conserved AAA + family ATPases that assemble and mature a plethora of macromolecular complexes and are pivotal in numerous cellular processes, especially by guaranteeing a co-chaperoning function within R2TP or R2TP-like machineries. In the present study, we identified DPCD as a new R1R2 partner in vivo. We show that DPCD interacts directly with R1 and R2 in vitro and in cells. We characterized the physico-chemical properties of DPCD in solution and built a 3D model of DPCD. In addition, we used a variety of orthogonal biophysical techniques including small-angle X-ray scattering, structural mass spectrometry and electron microscopy to assess the molecular determinants of DPCD interaction with R1R2. Interestingly, DPCD disrupts the dodecameric state of R1R2 complex upon binding and this interaction occurs mainly via the DII domains of R1R2.

Published
2022
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4. Author response: The final step of 40S ribosomal subunit maturation is controlled by a dual key lock

Author

Laura Plassart, Carole Pichereaux, Carine Froment, Marie-Françoise O'Donohue, Simon Lebaron, Christian Montellese, Pierre-Emmanuel Gleizes, Ulrike Kutay, Ramtin Shayan, Dana Rinaldi, Célia Plisson-Chastang, Natacha Larburu, and Julien Marcoux

Subjects
Chemistry, Protein subunit, Eukaryotic Small Ribosomal Subunit, Ribosomal RNA, Cell biology, Dual (category theory)
Published
2021
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5. The final step of 40S ribosomal subunit maturation is controlled by a dual key lock

Author

Christian Montellese, Ramtin Shayan, Pierre-Emmanuel Gleizes, Carine Froment, Julien Marcoux, Laura Plassart, Célia Plisson-Chastang, Simon Lebaron, Carole Pichereaux, Natacha Larburu, Marie-Françoise O'Donohue, Dana Rinaldi, Ulrike Kutay, Laboratoire de biologie moléculaire eucaryote (LBME), Centre National de la Recherche Scientifique (CNRS)-Centre de Biologie Intégrative (CBI), Université Toulouse III - Paul Sabatier (UT3), Université Fédérale Toulouse Midi-Pyrénées-Université Fédérale Toulouse Midi-Pyrénées-Centre National de la Recherche Scientifique (CNRS)-Université Toulouse III - Paul Sabatier (UT3), Université Fédérale Toulouse Midi-Pyrénées-Université Fédérale Toulouse Midi-Pyrénées-Centre National de la Recherche Scientifique (CNRS), and Centre de Biologie Intégrative (CBI)

Subjects
Ribosomal Proteins, QH301-705.5, Science, Structural Biology and Molecular Biophysics, [SDV]Life Sciences [q-bio], Protein subunit, Endoribonuclease, Cell Cycle Proteins, Protein Serine-Threonine Kinases, Cleavage (embryo), General Biochemistry, Genetics and Molecular Biology, 18S ribosomal RNA, structure-function study, 03 medical and health sciences, 0302 clinical medicine, Ribosomal protein, Humans, Eukaryotic Small Ribosomal Subunit, Biology (General), 030304 developmental biology, Ribosome Subunits, Small, Eukaryotic, human ribosome biogenesis, 0303 health sciences, General Immunology and Microbiology, Chemistry, General Neuroscience, Nuclear Proteins, RNA-Binding Proteins, General Medicine, Ribosomal RNA, Chromosomes and Gene Expression, Cell biology, Structural biology, Medicine, cryo-EM, small ribosomal subunit, pre-rRNA processing, 030217 neurology & neurosurgery, Research Article, Human
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., eLife, 10, ISSN:2050-084X

Published
2021
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6. The final step of 40S ribosomal subunit maturation is controlled by a dual key lock

Author

Laura Plassart, Simon Lebaron, Dana Rinaldi, Carole Pichereaux, Ramtin Shayan, Pierre-Emmanuel Gleizes, Natacha Larburu, Christian Montellese, Célia Plisson-Chastang, Julien Marcoux, Marie-Françoise O'Donohue, Ulrike Kutay, Centre National de la Recherche Scientifique (CNRS), Laboratoire de biologie moléculaire eucaryote (LBME), Centre National de la Recherche Scientifique (CNRS)-Centre de Biologie Intégrative (CBI), Université Toulouse III - Paul Sabatier (UT3), Université Fédérale Toulouse Midi-Pyrénées-Université Fédérale Toulouse Midi-Pyrénées-Centre National de la Recherche Scientifique (CNRS)-Université Toulouse III - Paul Sabatier (UT3), Université Fédérale Toulouse Midi-Pyrénées-Université Fédérale Toulouse Midi-Pyrénées-Centre National de la Recherche Scientifique (CNRS), and Centre de Biologie Intégrative (CBI)

Subjects
0303 health sciences, Chemistry, Protein subunit, [SDV]Life Sciences [q-bio], Endoribonuclease, Translation (biology), Ribosomal RNA, Cleavage (embryo), 18S ribosomal RNA, Cell biology, 03 medical and health sciences, 0302 clinical medicine, Ribosomal protein, Eukaryotic Small Ribosomal Subunit, 030217 neurology & neurosurgery, 030304 developmental biology
Abstract

Preventing premature interaction of preribosomes with the translation apparatus is essential to translation accuracy. Hence, the final maturation step releasing functional 40S ribosomal subunits, namely processing of the 18S ribosomal RNA 3′ end, is safeguarded by 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-EM analysis of late human pre-40S particles purified using a catalytically-inactive form of ATPase RIO1. These structures, together with in vivo and in vitro functional analyses, support a model in which ATPloaded 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.; Preventing premature interaction of preribosomes with the translation apparatus is essential to translation accuracy. Hence, the final maturation step releasing functional 40S ribosomal subunits, namely processing of the 18S ribosomal RNA 3′ end, is safeguarded by 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-EM analysis of late human pre-40S particles purified using a catalytically-inactive form of ATPase RIO1. These structures, together with in vivo and in vitro functional analyses, support a model in which ATPloaded 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.

Published
2020

7. Good vibrations: Structural remodeling of maturing yeast pre-40S ribosomal particles followed by cryo-electron microscopy

Author

Célia Plisson-Chastang, Natacha Larburu, Pierre-Emmanuel Gleizes, Ramtin Shayan, Laura Plassart, Dana Rinaldi, Julien Marcoux, Simon Lebaron, Stéphanie Balor, David Bouyssié, Laboratoire de biologie moléculaire eucaryote (LBME), Université Toulouse III - Paul Sabatier (UT3), Université Fédérale Toulouse Midi-Pyrénées-Université Fédérale Toulouse Midi-Pyrénées-Centre National de la Recherche Scientifique (CNRS)-Centre de Biologie Intégrative (CBI), Université Fédérale Toulouse Midi-Pyrénées-Université Fédérale Toulouse Midi-Pyrénées-Centre National de la Recherche Scientifique (CNRS)-Centre National de la Recherche Scientifique (CNRS), Centre de Biologie Intégrative (CBI), Université Fédérale Toulouse Midi-Pyrénées-Université Fédérale Toulouse Midi-Pyrénées-Centre National de la Recherche Scientifique (CNRS), Centre National de la Recherche Scientifique (CNRS)-Centre de Biologie Intégrative (CBI), Université Fédérale Toulouse Midi-Pyrénées-Université Fédérale Toulouse Midi-Pyrénées-Centre National de la Recherche Scientifique (CNRS)-Université Toulouse III - Paul Sabatier (UT3), Institut de pharmacologie et de biologie structurale (IPBS), Centre National de la Recherche Scientifique (CNRS)-Université Toulouse III - Paul Sabatier (UT3), and Université Fédérale Toulouse Midi-Pyrénées-Université Fédérale Toulouse Midi-Pyrénées

Subjects
Proteomics, [SDV]Life Sciences [q-bio], Pharmaceutical Science, Ribosome biogenesis, Ribosome, 18S ribosomal RNA, Article, Analytical Chemistry, Ribosome assembly, lcsh:QD241-441, 03 medical and health sciences, 0302 clinical medicine, lcsh:Organic chemistry, Ribosomal protein, Tandem Mass Spectrometry, [SDV.BBM.GTP]Life Sciences [q-bio]/Biochemistry, Molecular Biology/Genomics [q-bio.GN], Drug Discovery, RNA, Ribosomal, 18S, Eukaryotic Small Ribosomal Subunit, Physical and Theoretical Chemistry, single particle analysis, ComputingMilieux_MISCELLANEOUS, 030304 developmental biology, 0303 health sciences, [SDV.BBM.BS]Life Sciences [q-bio]/Biochemistry, Molecular Biology/Structural Biology [q-bio.BM], Chemistry, Organic Chemistry, Cryoelectron Microscopy, Computational Biology, Ribosomal RNA, 3. Good health, Cell biology, Ribosome Subunits, Small, Chemistry (miscellaneous), Molecular Medicine, cryo-EM, small ribosomal subunit, Eukaryotic Ribosome, ribosome assembly, bottom-up proteomics, Ribosomes, 030217 neurology & neurosurgery
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 &ldquo, resolution revolution&rdquo, 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 &ldquo, vibrating&rdquo, or &ldquo, wriggling&rdquo, 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.

Published
2020
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