51
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Chaker-Margot M, Klinge S. Assembly and early maturation of large subunit precursors. RNA (NEW YORK, N.Y.) 2019; 25:465-471. [PMID: 30670483 PMCID: PMC6426289 DOI: 10.1261/rna.069799.118] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 12/03/2018] [Accepted: 01/19/2019] [Indexed: 06/09/2023]
Abstract
The eukaryotic ribosome is assembled through a complex process involving more than 200 factors. As preribosomal RNA is transcribed, assembly factors bind the nascent pre-rRNA and guide its correct folding, modification, and cleavage. While these early events in the assembly of the small ribosomal subunit have been relatively well characterized, assembly of the large subunit precursors, or pre-60S, is less well understood. Recent structures of nucleolar intermediates of large subunit assembly have shed light on the role of many early large subunit assembly factors, but how these particles emerge is still unknown. Here, we use the expression and purification of truncated pre-rRNAs to examine the initial assembly of pre-60S particles. Using this approach, we can recapitulate the early recruitment of large subunit assembly factors mainly to the domains I, II, and VI of the assembling 25S rRNA.
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MESH Headings
- Aptamers, Nucleotide/chemical synthesis
- Aptamers, Nucleotide/metabolism
- Cloning, Molecular
- Organelle Biogenesis
- Plasmids/chemistry
- Plasmids/metabolism
- RNA Precursors/genetics
- RNA Precursors/metabolism
- RNA, Ribosomal/genetics
- RNA, Ribosomal/metabolism
- Ribosomal Proteins/genetics
- Ribosomal Proteins/metabolism
- Ribosome Subunits, Large, Eukaryotic/genetics
- Ribosome Subunits, Large, Eukaryotic/metabolism
- Ribosome Subunits, Large, Eukaryotic/ultrastructure
- Saccharomyces cerevisiae/genetics
- Saccharomyces cerevisiae/metabolism
- Staining and Labeling/methods
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Affiliation(s)
- Malik Chaker-Margot
- Laboratory of Protein and Nucleic Acid Chemistry, The Rockefeller University, New York, New York 10065, USA
- Tri-Institutional Training Program in Chemical Biology, The Rockefeller University, New York, New York 10065, USA
| | - Sebastian Klinge
- Laboratory of Protein and Nucleic Acid Chemistry, The Rockefeller University, New York, New York 10065, USA
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52
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Zhou Y, Musalgaonkar S, Johnson AW, Taylor DW. Tightly-orchestrated rearrangements govern catalytic center assembly of the ribosome. Nat Commun 2019; 10:958. [PMID: 30814529 PMCID: PMC6393466 DOI: 10.1038/s41467-019-08880-0] [Citation(s) in RCA: 41] [Impact Index Per Article: 8.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2018] [Accepted: 02/01/2019] [Indexed: 11/24/2022] Open
Abstract
The catalytic activity of the ribosome is mediated by RNA, yet proteins are essential for the function of the peptidyl transferase center (PTC). In eukaryotes, final assembly of the PTC occurs in the cytoplasm by insertion of the ribosomal protein Rpl10 (uL16). We determine structures of six intermediates in late nuclear and cytoplasmic maturation of the large subunit that reveal a tightly-choreographed sequence of protein and RNA rearrangements controlling the insertion of Rpl10. We also determine the structure of the biogenesis factor Yvh1 and show how it promotes assembly of the P stalk, a critical element for recruitment of GTPases that drive translation. Together, our structures provide a blueprint for final assembly of a functional ribosome. In eukaryotes, ribosome biogenesis culminates in the cytoplasm with the maturation of the peptidyl transfer center (PTC). Here the authors describe several structures of intermediates in late nuclear and cytoplasmic maturation of the large ribosomal subunit that reveal the tightly-choreographed sequence of protein and RNA rearrangements that lead to the completion of the PTC.
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Affiliation(s)
- Yi Zhou
- Department of Molecular Biosciences, University of Texas at Austin, Austin, TX, 78712, USA
| | | | - Arlen W Johnson
- Department of Molecular Biosciences, University of Texas at Austin, Austin, TX, 78712, USA. .,Institute for Cellular and Molecular Biology, University of Texas at Austin, Austin, TX, 78712, USA.
| | - David W Taylor
- Department of Molecular Biosciences, University of Texas at Austin, Austin, TX, 78712, USA.,Institute for Cellular and Molecular Biology, University of Texas at Austin, Austin, TX, 78712, USA.,Center for Systems and Synthetic Biology, University of Texas at Austin, Austin, TX, 78712, USA.,LIVESTRONG Cancer Institutes, Dell Medical School, Austin, TX, 78712, USA
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53
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Linnemann J, Pöll G, Jakob S, Ferreira-Cerca S, Griesenbeck J, Tschochner H, Milkereit P. Impact of two neighbouring ribosomal protein clusters on biogenesis factor binding and assembly of yeast late small ribosomal subunit precursors. PLoS One 2019; 14:e0203415. [PMID: 30653518 PMCID: PMC6336269 DOI: 10.1371/journal.pone.0203415] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/17/2018] [Accepted: 01/01/2019] [Indexed: 11/25/2022] Open
Abstract
Many of the small ribosomal subunit proteins are required for the stabilisation of late small ribosomal subunit (SSU) precursors and for final SSU rRNA processing in S. cerevisiae. Among them are ribosomal proteins (r-proteins) which form a protein cluster around rpS0 (uS2) at the "neck" of the SSU (S0-cluster) and others forming a nearby protein cluster around rpS3 (uS3) at the SSU "beak". Here we applied semi-quantitative proteomics together with complementary biochemical approaches to study how incomplete assembly of these two r-protein clusters affects binding and release of SSU maturation factors and assembly of other r-proteins in late SSU precursors in S. cerevisiae. For each of the two clusters specific impairment of the local r-protein assembly state was observed in Rio2 associated SSU precursors. Besides, cluster-specific effects on the association of biogenesis factors were detected. These suggested a role of S0-cluster formation for the efficient release of the two nuclear export factors Rrp12 and Slx9 from SSU precursors and for the correct incorporation of the late acting biogenesis factor Rio2. Based on our and on previous results we propose the existence of at least two different r-protein assembly checkpoints during late SSU maturation in S. cerevisiae. We discuss in the light of recent SSU precursor structure models how r-protein assembly states might be sensed by biogenesis factors at the S0-cluster checkpoint.
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Affiliation(s)
- Jan Linnemann
- Lehrstuhl für Biochemie III, Universität Regensburg, Regensburg, Germany
| | - Gisela Pöll
- Lehrstuhl für Biochemie III, Universität Regensburg, Regensburg, Germany
| | - Steffen Jakob
- Lehrstuhl für Biochemie III, Universität Regensburg, Regensburg, Germany
| | | | - Joachim Griesenbeck
- Lehrstuhl für Biochemie III, Universität Regensburg, Regensburg, Germany
- * E-mail: (JG); (HT); (PM)
| | - Herbert Tschochner
- Lehrstuhl für Biochemie III, Universität Regensburg, Regensburg, Germany
- * E-mail: (JG); (HT); (PM)
| | - Philipp Milkereit
- Lehrstuhl für Biochemie III, Universität Regensburg, Regensburg, Germany
- * E-mail: (JG); (HT); (PM)
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54
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Abstract
Ribosomes, which synthesize the proteins of a cell, comprise ribosomal RNA and ribosomal proteins, which coassemble hierarchically during a process termed ribosome biogenesis. Historically, biochemical and molecular biology approaches have revealed how preribosomal particles form and mature in consecutive steps, starting in the nucleolus and terminating after nuclear export into the cytoplasm. However, only recently, due to the revolution in cryo-electron microscopy, could pseudoatomic structures of different preribosomal particles be obtained. Together with in vitro maturation assays, these findings shed light on how nascent ribosomes progress stepwise along a dynamic biogenesis pathway. Preribosomes assemble gradually, chaperoned by a myriad of assembly factors and small nucleolar RNAs, before they reach maturity and enter translation. This information will lead to a better understanding of how ribosome synthesis is linked to other cellular pathways in humans and how it can cause diseases, including cancer, if disturbed.
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Affiliation(s)
- Jochen Baßler
- Biochemistry Center, University of Heidelberg, 69120 Heidelberg, Germany; ,
| | - Ed Hurt
- Biochemistry Center, University of Heidelberg, 69120 Heidelberg, Germany; ,
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55
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Thoms M, Mitterer V, Kater L, Falquet L, Beckmann R, Kressler D, Hurt E. Suppressor mutations in Rpf2-Rrs1 or Rpl5 bypass the Cgr1 function for pre-ribosomal 5S RNP-rotation. Nat Commun 2018; 9:4094. [PMID: 30291245 PMCID: PMC6173701 DOI: 10.1038/s41467-018-06660-w] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/26/2018] [Accepted: 09/17/2018] [Indexed: 12/03/2022] Open
Abstract
During eukaryotic 60S biogenesis, the 5S RNP requires a large rotational movement to achieve its mature position. Cryo-EM of the Rix1-Rea1 pre-60S particle has revealed the post-rotation stage, in which a gently undulating α-helix corresponding to Cgr1 becomes wedged between Rsa4 and the relocated 5S RNP, but the purpose of this insertion was unknown. Here, we show that cgr1 deletion in yeast causes a slow-growth phenotype and reversion of the pre-60S particle to the pre-rotation stage. However, spontaneous extragenic suppressors could be isolated, which restore growth and pre-60S biogenesis in the absence of Cgr1. Whole-genome sequencing reveals that the suppressor mutations map in the Rpf2–Rrs1 module and Rpl5, which together stabilize the unrotated stage of the 5S RNP. Thus, mutations in factors stabilizing the pre-rotation stage facilitate 5S RNP relocation upon deletion of Cgr1, but Cgr1 itself could stabilize the post-rotation stage. During biogenesis of the eukaryotic 60S ribosome, a large rotational movement of the 5S RNP is required to achieve its mature position. By analyzing extragenic suppressors of crg1—a key factor required for rotation—the authors provide mechanistic insight into a key step of ribosome biogenesis.
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Affiliation(s)
- Matthias Thoms
- Biochemistry Centre, University of Heidelberg, Heidelberg, 69120, Germany.
| | - Valentin Mitterer
- Biochemistry Centre, University of Heidelberg, Heidelberg, 69120, Germany
| | - Lukas Kater
- Gene Center, University of Munich, Munich, 81377, Germany
| | - Laurent Falquet
- University of Fribourg and Swiss Institute of Bioinformatics, Fribourg, 1700, Switzerland
| | | | - Dieter Kressler
- University of Fribourg and Swiss Institute of Bioinformatics, Fribourg, 1700, Switzerland
| | - Ed Hurt
- Biochemistry Centre, University of Heidelberg, Heidelberg, 69120, Germany.
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56
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Black JJ, Wang Z, Goering LM, Johnson AW. Utp14 interaction with the small subunit processome. RNA (NEW YORK, N.Y.) 2018; 24:1214-1228. [PMID: 29925570 PMCID: PMC6097655 DOI: 10.1261/rna.066373.118] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 03/12/2018] [Accepted: 06/17/2018] [Indexed: 06/08/2023]
Abstract
The SSU processome (sometimes referred to as 90S) is an early stable intermediate in the small ribosomal subunit biogenesis pathway of eukaryotes. Progression of the SSU processome to a pre-40S particle requires a large-scale compaction of the RNA and release of many biogenesis factors. The U3 snoRNA is a primary component of the SSU processome and hybridizes to the rRNA at multiple locations to organize the structure of the SSU processome. Thus, release of U3 is a prerequisite for the transition to pre-40S. Our laboratory proposed that the RNA helicase Dhr1 plays a crucial role in the transition by unwinding U3 and that this activity is controlled by the SSU processome protein Utp14. How Utp14 times the activation of Dhr1 is an open question. Despite being highly conserved, Utp14 contains no recognizable domains, and how Utp14 interacts with the SSU processome is not well characterized. Here, we used UV crosslinking and analysis of cDNA (CRAC) and yeast two-hybrid interaction to characterize how Utp14 interacts with the preribosome. Moreover, proteomic analysis of SSU particles lacking Utp14 revealed that the presence of Utp14 is needed for efficient recruitment of the RNA exosome. Our analysis positions Utp14 to be uniquely poised to communicate the status of assembly of the SSU processome to Dhr1 and possibly to the exosome as well.
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Affiliation(s)
- Joshua J Black
- Department of Molecular Biosciences, The University of Texas at Austin, Austin, Texas 78712, USA
| | - Zhaohui Wang
- Department of Molecular Biosciences, The University of Texas at Austin, Austin, Texas 78712, USA
| | - Lisa M Goering
- Department of Biological Sciences, St. Edward's University, Austin, Texas 78704, USA
| | - Arlen W Johnson
- Department of Molecular Biosciences, The University of Texas at Austin, Austin, Texas 78712, USA
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57
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Chaker-Margot M. Assembly of the small ribosomal subunit in yeast: mechanism and regulation. RNA (NEW YORK, N.Y.) 2018; 24:881-891. [PMID: 29712726 PMCID: PMC6004059 DOI: 10.1261/rna.066985.118] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/05/2023]
Abstract
The eukaryotic ribosome is made of four intricately folded ribosomal RNAs and 79 proteins. During rapid growth, yeast cells produce an incredible 2000 ribosomes every minute. Ribosome assembly involves more than 200 trans-acting factors, intervening from the transcription of the preribosomal RNA in the nucleolus to late maturation events in the cytoplasm. The biogenesis of the small ribosomal subunit, or 40S, is especially intricate, requiring more than four times the mass of the small subunit in assembly factors for its full maturation. Recent studies have provided new insights into the complex assembly of the 40S subunit. These data from cryo-electron microscopy, X-ray crystallography, and other biochemical and molecular biology methods, have elucidated the role of many factors required in small subunit maturation. Mechanisms of the regulation of ribosome assembly have also emerged from this body of work. This review aims to integrate these new results into an updated view of small subunit biogenesis and its regulation, in yeast, from transcription to the formation of the mature small subunit.
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Affiliation(s)
- Malik Chaker-Margot
- The Rockefeller University, New York, New York 10065, USA
- Tri-Institutional Program in Chemical Biology, New York, New York 10065, USA
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58
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Choque E, Schneider C, Gadal O, Dez C. Turnover of aberrant pre-40S pre-ribosomal particles is initiated by a novel endonucleolytic decay pathway. Nucleic Acids Res 2018; 46:4699-4714. [PMID: 29481617 PMCID: PMC5961177 DOI: 10.1093/nar/gky116] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/22/2017] [Revised: 01/29/2018] [Accepted: 02/09/2018] [Indexed: 01/05/2023] Open
Abstract
Ribosome biogenesis requires more than 200 trans-acting factors to achieve the correct production of the two mature ribosomal subunits. Here, we have identified Efg1 as a novel, nucleolar ribosome biogenesis factor in Saccharomyces cerevisiae that is directly linked to the surveillance of pre-40S particles. Depletion of Efg1 impairs early pre-rRNA processing, leading to a strong decrease in 18S rRNA and 40S subunit levels and an accumulation of the aberrant 23S rRNA. Using Efg1 as bait, we revealed a novel degradation pathway of the 23S rRNA. Co-immunoprecipitation experiments showed that Efg1 is a component of 90S pre-ribosomes, as it is associated with the 35S pre-rRNA and U3 snoRNA, but has stronger affinity for 23S pre-rRNA and its novel degradation intermediate 11S rRNA. 23S is cleaved at a new site, Q1, within the 18S sequence by the endonuclease Utp24, generating 11S and 17S' rRNA. Both of these cleavage products are targeted for degradation by the TRAMP/exosome complexes. Therefore, the Q1 site defines a novel endonucleolytic cleavage site of ribosomal RNA exclusively dedicated to surveillance of pre-ribosomal particles.
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Affiliation(s)
- Elodie Choque
- Laboratoire de Biologie Moléculaire Eucaryote, Centre de Biologie Intégrative (CBI), Université de Toulouse, CNRS, UPS, Toulouse Cedex 9, France
| | - Claudia Schneider
- Institute for Cell and Molecular Biosciences, Newcastle University, Newcastle upon Tyne NE2 4HH, UK
| | - Olivier Gadal
- Laboratoire de Biologie Moléculaire Eucaryote, Centre de Biologie Intégrative (CBI), Université de Toulouse, CNRS, UPS, Toulouse Cedex 9, France
| | - Christophe Dez
- Laboratoire de Biologie Moléculaire Eucaryote, Centre de Biologie Intégrative (CBI), Université de Toulouse, CNRS, UPS, Toulouse Cedex 9, France
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59
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An W, Du Y, Ye K. Structural and functional analysis of Utp24, an endonuclease for processing 18S ribosomal RNA. PLoS One 2018; 13:e0195723. [PMID: 29641590 PMCID: PMC5895043 DOI: 10.1371/journal.pone.0195723] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/03/2018] [Accepted: 03/28/2018] [Indexed: 01/05/2023] Open
Abstract
The precursor ribosomal RNA is processed by multiple steps of nucleolytic cleavage to generate mature rRNAs. Utp24 is a PIN domain endonuclease in the early 90S precursor of small ribosomal subunit and is proposed to cleave at sites A1 and A2 of pre-rRNA. Here we determine the crystal structure of Utp24 from Schizosaccharomyces pombe at 2.1 angstrom resolution. Utp24 structurally resembles the ribosome assembly factor Utp23 and both contain a Zn-finger motif. Functional analysis in Saccharomyces cerevisiae shows that depletion of Utp24 disturbs the assembly of 90S and abolishes cleavage at sites A0, A1 and A2. The 90S assembled with inactivated Utp24 is arrested at a post-A0-cleavage state and contains enriched nuclear exosome for degradation of 5' ETS. Despite of high sequence conservation, Utp24 from other organisms is unable to form an active 90S in S. cerevisiae, suggesting that Utp24 needs to be precisely positioned in 90S. Our study provides biochemical and structural insight into the role of Utp24 in 90S assembly and activity.
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Affiliation(s)
- Weidong An
- College of Biological Sciences, China Agricultural University, Beijing, China
- National Institute of Biological Sciences, Beijing, China
- Key Laboratory of RNA Biology, CAS Center for Excellence in Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing, China
| | - Yifei Du
- Key Laboratory of RNA Biology, CAS Center for Excellence in Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Keqiong Ye
- Key Laboratory of RNA Biology, CAS Center for Excellence in Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing, China
- University of Chinese Academy of Sciences, Beijing, China
- * E-mail:
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60
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Zisser G, Ohmayer U, Mauerhofer C, Mitterer V, Klein I, Rechberger GN, Wolinski H, Prattes M, Pertschy B, Milkereit P, Bergler H. Viewing pre-60S maturation at a minute's timescale. Nucleic Acids Res 2018; 46:3140-3151. [PMID: 29294095 PMCID: PMC5888160 DOI: 10.1093/nar/gkx1293] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/22/2017] [Revised: 11/30/2017] [Accepted: 12/18/2017] [Indexed: 12/03/2022] Open
Abstract
The formation of ribosomal subunits is a highly dynamic process that is initiated in the nucleus and involves more than 200 trans-acting factors, some of which accompany the pre-ribosomes into the cytoplasm and have to be recycled into the nucleus. The inhibitor diazaborine prevents cytoplasmic release and recycling of shuttling pre-60S maturation factors by inhibiting the AAA-ATPase Drg1. The failure to recycle these proteins results in their depletion in the nucleolus and halts the pathway at an early maturation step. Here, we made use of the fast onset of inhibition by diazaborine to chase the maturation path in real-time from 27SA2 pre-rRNA containing pre-ribosomes localized in the nucleolus up to nearly mature 60S subunits shortly after their export into the cytoplasm. This allows for the first time to put protein assembly and disassembly reactions as well as pre-rRNA processing into a chronological context unraveling temporal and functional linkages during ribosome maturation.
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Affiliation(s)
- Gertrude Zisser
- Institute of Molecular Biosciences, Humboldtstrasse 50/EG, University of Graz, A-8010 Graz, Austria
| | - Uli Ohmayer
- Lehrstuhl Biochemie III, University Regensburg, Universitätsstrasse 31, 93053 Regensburg, Germany
| | - Christina Mauerhofer
- Institute of Molecular Biosciences, Humboldtstrasse 50/EG, University of Graz, A-8010 Graz, Austria
| | - Valentin Mitterer
- Institute of Molecular Biosciences, Humboldtstrasse 50/EG, University of Graz, A-8010 Graz, Austria
| | - Isabella Klein
- Institute of Molecular Biosciences, Humboldtstrasse 50/EG, University of Graz, A-8010 Graz, Austria
| | - Gerald N Rechberger
- Institute of Molecular Biosciences, Humboldtstrasse 50/EG, University of Graz, A-8010 Graz, Austria
- Omics Center Graz, BioTechMed-Graz, A-8010 Graz, Austria
| | - Heimo Wolinski
- Institute of Molecular Biosciences, Humboldtstrasse 50/EG, University of Graz, A-8010 Graz, Austria
- BioTechMed-Graz, A-8010 Graz, Austria
| | - Michael Prattes
- Institute of Molecular Biosciences, Humboldtstrasse 50/EG, University of Graz, A-8010 Graz, Austria
| | - Brigitte Pertschy
- Institute of Molecular Biosciences, Humboldtstrasse 50/EG, University of Graz, A-8010 Graz, Austria
- BioTechMed-Graz, A-8010 Graz, Austria
| | - Philipp Milkereit
- Lehrstuhl Biochemie III, University Regensburg, Universitätsstrasse 31, 93053 Regensburg, Germany
| | - Helmut Bergler
- Institute of Molecular Biosciences, Humboldtstrasse 50/EG, University of Graz, A-8010 Graz, Austria
- BioTechMed-Graz, A-8010 Graz, Austria
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61
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Zhou D, Zhu X, Zheng S, Tan D, Dong MQ, Ye K. Cryo-EM structure of an early precursor of large ribosomal subunit reveals a half-assembled intermediate. Protein Cell 2018; 10:120-130. [PMID: 29557065 PMCID: PMC6340896 DOI: 10.1007/s13238-018-0526-7] [Citation(s) in RCA: 54] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/09/2018] [Accepted: 03/04/2018] [Indexed: 11/25/2022] Open
Abstract
Assembly of eukaryotic ribosome is a complicated and dynamic process that involves a series of intermediates. It is unknown how the highly intertwined structure of 60S large ribosomal subunits is established. Here, we report the structure of an early nucleolar pre-60S ribosome determined by cryo-electron microscopy at 3.7 Å resolution, revealing a half-assembled subunit. Domains I, II and VI of 25S/5.8S rRNA pack tightly into a native-like substructure, but domains III, IV and V are not assembled. The structure contains 12 assembly factors and 19 ribosomal proteins, many of which are required for early processing of large subunit rRNA. The Brx1-Ebp2 complex would interfere with the assembly of domains IV and V. Rpf1, Mak16, Nsa1 and Rrp1 form a cluster that consolidates the joining of domains I and II. Our structure reveals a key intermediate on the path to establishing the global architecture of 60S subunits.
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Affiliation(s)
- Dejian Zhou
- Graduate School of Peking Union Medical College and Chinese Academy of Medical Sciences, Beijing, 100730, China.,Key Laboratory of RNA Biology, Institute of Biophysics, CAS Center for Excellence in Biomacromolecules, Chinese Academy of Sciences, Beijing, 100101, China.,National Institute of Biological Sciences, Beijing, 102206, China
| | - Xing Zhu
- Key Laboratory of RNA Biology, Institute of Biophysics, CAS Center for Excellence in Biomacromolecules, Chinese Academy of Sciences, Beijing, 100101, China
| | - Sanduo Zheng
- National Institute of Biological Sciences, Beijing, 102206, China
| | - Dan Tan
- National Institute of Biological Sciences, Beijing, 102206, China
| | - Meng-Qiu Dong
- National Institute of Biological Sciences, Beijing, 102206, China
| | - Keqiong Ye
- Graduate School of Peking Union Medical College and Chinese Academy of Medical Sciences, Beijing, 100730, China. .,Key Laboratory of RNA Biology, Institute of Biophysics, CAS Center for Excellence in Biomacromolecules, Chinese Academy of Sciences, Beijing, 100101, China. .,University of Chinese Academy of Sciences, Beijing, 100049, China.
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62
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Assembly and structure of the SSU processome-a nucleolar precursor of the small ribosomal subunit. Curr Opin Struct Biol 2018; 49:85-93. [PMID: 29414516 DOI: 10.1016/j.sbi.2018.01.008] [Citation(s) in RCA: 57] [Impact Index Per Article: 9.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/11/2017] [Revised: 01/11/2018] [Accepted: 01/12/2018] [Indexed: 12/22/2022]
Abstract
The small subunit processome is the first precursor of the small eukaryotic ribosomal subunit. During its assembly in the nucleolus, many ribosome biogenesis factors, an RNA chaperone, and ribosomal proteins associate with the nascent pre-rRNA. Biochemical studies have elucidated the rRNA-subdomain dependent recruitment of these factors during SSU processome assembly and have been complemented by structural studies of the assembled particle. Ribosome biogenesis factors encapsulate and guide subdomains of pre-ribosomal RNA in distinct compartments. This prevents uncoordinated maturation and enables processing of regions not accessible in the mature subunit. By sequentially reducing conformational freedom, flexible proteins facilitate the incorporation of dynamic subcomplexes into a globular particle. Large rearrangements within the SSU processome are required for compaction into the mature small ribosomal subunit.
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63
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Vincent NG, Charette JM, Baserga SJ. The SSU processome interactome in Saccharomyces cerevisiae reveals novel protein subcomplexes. RNA (NEW YORK, N.Y.) 2018; 24:77-89. [PMID: 29054886 PMCID: PMC5733573 DOI: 10.1261/rna.062927.117] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/11/2017] [Accepted: 10/03/2017] [Indexed: 05/05/2023]
Abstract
Ribosome assembly is an evolutionarily conserved and energy intensive process required for cellular growth, proliferation, and maintenance. In yeast, assembly of the small ribosomal subunit (SSU) requires approximately 75 assembly factors that act in coordination to form the SSU processome, a 6 MDa ribonucleoprotein complex. The SSU processome is required for processing, modifying, and folding the preribosomal RNA (rRNA) to prepare it for incorporation into the mature SSU. Although the protein composition of the SSU processome has been known for some time, the interaction network of the proteins required for its assembly has remained poorly defined. Here, we have used a semi-high-throughput yeast two-hybrid (Y2H) assay and coimmunoprecipitation validation method to produce a high-confidence interactome of SSU processome assembly factors (SPAFs), providing essential insight into SSU assembly and ribosome biogenesis. Further, we used glycerol density-gradient sedimentation to reveal the presence of protein subcomplexes that have not previously been observed. Our work not only provides essential insight into SSU assembly and ribosome biogenesis, but also serves as an important resource for future investigations into how defects in biogenesis and assembly cause congenital disorders of ribosomes known as ribosomopathies.
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Affiliation(s)
- Nicholas G Vincent
- Department of Microbiology, Yale University School of Medicine, New Haven, Connecticut 06520, USA
| | - J Michael Charette
- Department of Molecular Biophysics and Biochemistry, Yale University School of Medicine, New Haven, Connecticut 06520, USA
| | - Susan J Baserga
- Department of Molecular Biophysics and Biochemistry, Yale University School of Medicine, New Haven, Connecticut 06520, USA
- Department of Genetics, Yale University School of Medicine, New Haven, Connecticut, 06520, USA
- Department of Therapeutic Radiology, Yale University School of Medicine, New Haven, Connecticut 06520, USA
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64
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Hu J, Zhu X, Ye K. Structure and RNA recognition of ribosome assembly factor Utp30. RNA (NEW YORK, N.Y.) 2017; 23:1936-1945. [PMID: 28951391 PMCID: PMC5689012 DOI: 10.1261/rna.062695.117] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 06/26/2017] [Accepted: 09/21/2017] [Indexed: 06/07/2023]
Abstract
The 90S preribosomes are gigantic early assembly intermediates of small ribosomal subunits. Cryo-EM structures of 90S were recently determined, but many of its components have not been accurately modeled. Here we determine the crystal structure of yeast Utp30, a ribosomal L1 domain-containing protein in 90S, at 2.65 Å resolution, revealing a classic two-domain fold. The structure of Utp30 fits well into the cryo-EM density of 90S, confirming its previously assigned location. Utp30 binds to the rearranged helix 41 of 18S rRNA and helix 4 of 5' external transcribed spacer in 90S. Comparison of RNA-binding modes of different L1 domains illustrates that they consistently recognize a short RNA duplex with the concaved surface of domain I, but are versatile in RNA recognition outside the core interface. Cic1 is a paralog of Utp30 associating with large subunit preribosomes. Utp30 and Cic1 share similar RNA-binding modes, suggesting that their distinct functions may be executed by a single protein in other organisms. Deletion of Utp30 does not affect the composition of 90S. The nonessential role of Utp30 could be ascribed to its peripheral localization and redundant interactions in 90S.
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Affiliation(s)
- Jianfei Hu
- Key Laboratory of RNA Biology, CAS Center for Excellence in Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing 100101, China
- Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai 201203, China
- School of Life Science and Technology, ShanghaiTech University, Shanghai 201210, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Xing Zhu
- Key Laboratory of RNA Biology, CAS Center for Excellence in Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing 100101, China
| | - Keqiong Ye
- Key Laboratory of RNA Biology, CAS Center for Excellence in Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing 100101, China
- University of Chinese Academy of Sciences, Beijing 100049, China
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65
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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] [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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66
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Chen W, Xie Z, Yang F, Ye K. Stepwise assembly of the earliest precursors of large ribosomal subunits in yeast. Nucleic Acids Res 2017; 45:6837-6847. [PMID: 28402444 PMCID: PMC5499802 DOI: 10.1093/nar/gkx254] [Citation(s) in RCA: 41] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/19/2017] [Accepted: 04/04/2017] [Indexed: 12/15/2022] Open
Abstract
Small ribosomal subunits are co-transcriptionally assembled on the nascent precursor rRNA in Saccharomyces cerevisiae. It is unknown how the highly intertwined structure of 60S large ribosomal subunits is initially formed. Here, we affinity purified and analyzed a series of pre-60S particles assembled in vivo on plasmid-encoded pre-rRNA fragments of increasing lengths, revealing a spatiotemporal assembly map for 34 trans-acting assembly factors (AFs), 30 ribosomal proteins and 5S rRNA. The gradual association of AFs and ribosomal proteins with the pre-rRNA fragments strongly supports that the pre-60S is co-transcriptionally, rather than post-transcriptionally, assembled. The internal and external transcribed spacers ITS1, ITS2 and 3΄ ETS in pre-rRNA must be processed in pre-60S. We show that the processing machineries for ITS1 and ITS2 are primarily recruited by the 5΄ and 3΄ halves of pre-27S RNA, respectively. Nevertheless, processing of both ITS1 and ITS2 requires a complete 25S region. The 3΄ ETS plays a minor role in ribosome assembly, but is important for efficient rRNA processing and ribosome maturation. We also identified a distinct pre-60S state occurring before ITS2 processing. Our data reveal the elusive co-transcriptional assembly pathway of large ribosomal subunit.
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Affiliation(s)
- Wu Chen
- College of Biological Sciences, China Agricultural University, Beijing 100193, China.,National Institute of Biological Sciences, Beijing 102206, China.,Key Laboratory of RNA Biology, CAS Center for Excellence in Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing 100101, China
| | - Zhensheng Xie
- Laboratory of Proteomics, Institute of Biophysics, Chinese Academy of Sciences, Beijing 100101, China.,University of Chinese Academy of Sciences, Beijing 100049, China
| | - Fuquan Yang
- Laboratory of Proteomics, Institute of Biophysics, Chinese Academy of Sciences, Beijing 100101, China.,University of Chinese Academy of Sciences, Beijing 100049, China
| | - Keqiong Ye
- Key Laboratory of RNA Biology, CAS Center for Excellence in Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing 100101, China.,University of Chinese Academy of Sciences, Beijing 100049, China
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67
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Barandun J, Chaker-Margot M, Hunziker M, Molloy KR, Chait BT, Klinge S. The complete structure of the small-subunit processome. Nat Struct Mol Biol 2017; 24:944-953. [PMID: 28945246 DOI: 10.1038/nsmb.3472] [Citation(s) in RCA: 99] [Impact Index Per Article: 14.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2017] [Accepted: 08/25/2017] [Indexed: 01/24/2023]
Abstract
The small-subunit processome represents the earliest stable precursor of the eukaryotic small ribosomal subunit. Here we present the cryo-EM structure of the Saccharomyces cerevisiae small-subunit processome at an overall resolution of 3.8 Å, which provides an essentially complete near-atomic model of this assembly. In this nucleolar superstructure, 51 ribosome-assembly factors and two RNAs encapsulate the 18S rRNA precursor and 15 ribosomal proteins in a state that precedes pre-rRNA cleavage at site A1. Extended flexible proteins are employed to connect distant sites in this particle. Molecular mimicry and steric hindrance, as well as protein- and RNA-mediated RNA remodeling, are used in a concerted fashion to prevent the premature formation of the central pseudoknot and its surrounding elements within the small ribosomal subunit.
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Affiliation(s)
- Jonas Barandun
- Laboratory of Protein and Nucleic Acid Chemistry, The Rockefeller University, New York, New York, USA
| | - Malik Chaker-Margot
- Laboratory of Protein and Nucleic Acid Chemistry, The Rockefeller University, New York, New York, USA
- Tri-Institutional Training Program in Chemical Biology, The Rockefeller University, New York, New York, USA
| | - Mirjam Hunziker
- Laboratory of Protein and Nucleic Acid Chemistry, The Rockefeller University, New York, New York, USA
| | - Kelly R Molloy
- Laboratory of Mass Spectrometry and Gaseous Ion Chemistry, The Rockefeller University, New York, New York, USA
| | - Brian T Chait
- Laboratory of Mass Spectrometry and Gaseous Ion Chemistry, The Rockefeller University, New York, New York, USA
| | - Sebastian Klinge
- Laboratory of Protein and Nucleic Acid Chemistry, The Rockefeller University, New York, New York, USA
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68
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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 2017; 24:954-964. [PMID: 28967883 DOI: 10.1038/nsmb.3476] [Citation(s) in RCA: 86] [Impact Index Per Article: 12.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/10/2017] [Accepted: 09/04/2017] [Indexed: 12/15/2022]
Abstract
The 40S small ribosomal subunit is cotranscriptionally assembled in the nucleolus as part of a large chaperone complex called the 90S preribosome or small-subunit processome. Here, we present the 3.2-Å-resolution structure of the Chaetomium thermophilum 90S preribosome, which allowed us to build atomic structures for 34 assembly factors, including the Mpp10 complex, Bms1, Utp14 and Utp18, and the complete U3 small nucleolar ribonucleoprotein. Moreover, we visualized the U3 RNA heteroduplexes with a 5' external transcribed spacer (5' ETS) and pre-18S RNA, and their stabilization by 90S factors. Overall, the structure explains how a highly intertwined network of assembly factors and pre-rRNA guide the sequential, independent folding of the individual pre-40S domains while the RNA regions forming the 40S active sites are kept immature. Finally, by identifying the unprocessed A1 cleavage site and the nearby Utp24 endonuclease, we suggest a proofreading model for regulated 5'-ETS separation and 90S-pre-40S transition.
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Affiliation(s)
- Jingdong Cheng
- Gene Center Munich and Center of Integrated Protein Science-Munich (CiPS-M), Department of Biochemistry, University of Munich, Munich, Germany
| | - Nikola Kellner
- Biochemie-Zentrum der Universität Heidelberg, Heidelberg, Germany
| | - Otto Berninghausen
- Gene Center Munich and Center of Integrated Protein Science-Munich (CiPS-M), Department of Biochemistry, University of Munich, Munich, Germany
| | - Ed Hurt
- Biochemie-Zentrum der Universität Heidelberg, Heidelberg, Germany
| | - Roland Beckmann
- Gene Center Munich and Center of Integrated Protein Science-Munich (CiPS-M), Department of Biochemistry, University of Munich, Munich, Germany
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69
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Eukaryotic ribosome assembly, transport and quality control. Nat Struct Mol Biol 2017; 24:689-699. [PMID: 28880863 DOI: 10.1038/nsmb.3454] [Citation(s) in RCA: 159] [Impact Index Per Article: 22.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/06/2017] [Accepted: 07/27/2017] [Indexed: 12/18/2022]
Abstract
Eukaryotic ribosome synthesis is a complex, energy-consuming process that takes place across the nucleolus, nucleoplasm and cytoplasm and requires more than 200 conserved assembly factors. Here, we discuss mechanisms by which the ribosome assembly and nucleocytoplasmic transport machineries collaborate to produce functional ribosomes. We also highlight recent cryo-EM studies that provided unprecedented snapshots of ribosomes during assembly and quality control.
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70
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Moriggi G, Gaspar SG, Nieto B, Bustelo XR, Dosil M. Focal accumulation of preribosomes outside the nucleolus during metaphase-anaphase in budding yeast. RNA (NEW YORK, N.Y.) 2017; 23:1432-1443. [PMID: 28588079 PMCID: PMC5558912 DOI: 10.1261/rna.061259.117] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 02/24/2017] [Accepted: 05/30/2017] [Indexed: 06/07/2023]
Abstract
Saccharomyces cerevisiae contains one nucleolus that remains intact in the mother-cell side of the nucleus throughout most of mitosis. Based on this, it is assumed that the bulk of ribosome production during cell division occurs in the mother cell. Here, we show that the ribosome synthesis machinery localizes not only in the nucleolus but also at a center that is present in the bud side of the nucleus after the initiation of mitosis. This center can be visualized by live microscopy as a punctate body located in close proximity to the nuclear envelope and opposite to the nucleolus. It contains ribosomal DNA (rDNA) and precursors of both 40S and 60S ribosomal subunits. Proteins that actively participate in ribosome synthesis, but not functionally defective variants, accumulate in that site. The formation of this body occurs in the metaphase-to-anaphase transition when discrete regions of rDNA occasionally exit the nucleolus and move into the bud. Collectively, our data unveil the existence of a previously unknown mechanism for preribosome accumulation at the nuclear periphery in budding yeast. We propose that this might be a strategy to expedite the delivery of ribosomes to the growing bud.
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Affiliation(s)
- Giulia Moriggi
- Centro de Investigación del Cáncer and Instituto de Biología Molecular y Celular del Cáncer, CSIC-University of Salamanca, 37007 Salamanca, Spain
| | - Sonia G Gaspar
- Centro de Investigación del Cáncer and Instituto de Biología Molecular y Celular del Cáncer, CSIC-University of Salamanca, 37007 Salamanca, Spain
| | - Blanca Nieto
- Centro de Investigación del Cáncer and Instituto de Biología Molecular y Celular del Cáncer, CSIC-University of Salamanca, 37007 Salamanca, Spain
| | - Xosé R Bustelo
- Centro de Investigación del Cáncer and Instituto de Biología Molecular y Celular del Cáncer, CSIC-University of Salamanca, 37007 Salamanca, Spain
- Centro de Investigación Biomédica en Red de Cáncer (CIBERONC), Centro de Investigación del Cáncer, 37007 Salamanca, Spain
| | - Mercedes Dosil
- Centro de Investigación del Cáncer and Instituto de Biología Molecular y Celular del Cáncer, CSIC-University of Salamanca, 37007 Salamanca, Spain
- Departamento de Bioquímica y Biología Molecular, University of Salamanca, 37007 Salamanca, Spain
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71
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Sá-Moura B, Kornprobst M, Kharde S, Ahmed YL, Stier G, Kunze R, Sinning I, Hurt E. Mpp10 represents a platform for the interaction of multiple factors within the 90S pre-ribosome. PLoS One 2017; 12:e0183272. [PMID: 28813493 PMCID: PMC5558966 DOI: 10.1371/journal.pone.0183272] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/08/2017] [Accepted: 08/01/2017] [Indexed: 11/29/2022] Open
Abstract
In eukaryotes, ribosome assembly is a highly complex process that involves more than 200 assembly factors that ensure the folding, modification and processing of the different rRNA species as well as the timely association of ribosomal proteins. One of these factors, Mpp10 associates with Imp3 and Imp4 to form a complex that is essential for the normal production of the 18S rRNA. Here we report the crystal structure of a complex between Imp4 and a short helical element of Mpp10 to a resolution of 1.88 Å. Furthermore, we extend the interaction network of Mpp10 and characterize two novel interactions. Mpp10 is able to bind the ribosome biogenesis factor Utp3/Sas10 through two conserved motifs in its N-terminal region. In addition, Mpp10 interacts with the ribosomal protein S5/uS7 using a short stretch within an acidic loop region. Thus, our findings reveal that Mpp10 provides a platform for the simultaneous interaction with multiple proteins in the 90S pre-ribosome.
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Affiliation(s)
- Bebiana Sá-Moura
- Biochemistry Center Heidelberg BZH, University of Heidelberg, Heidelberg, Germany
| | - Markus Kornprobst
- Biochemistry Center Heidelberg BZH, University of Heidelberg, Heidelberg, Germany
| | - Satyavati Kharde
- Biochemistry Center Heidelberg BZH, University of Heidelberg, Heidelberg, Germany
| | - Yasar Luqman Ahmed
- Biochemistry Center Heidelberg BZH, University of Heidelberg, Heidelberg, Germany
| | - Gunter Stier
- Biochemistry Center Heidelberg BZH, University of Heidelberg, Heidelberg, Germany
| | - Ruth Kunze
- Biochemistry Center Heidelberg BZH, University of Heidelberg, Heidelberg, Germany
| | - Irmgard Sinning
- Biochemistry Center Heidelberg BZH, University of Heidelberg, Heidelberg, Germany
| | - Ed Hurt
- Biochemistry Center Heidelberg BZH, University of Heidelberg, Heidelberg, Germany
- * E-mail:
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72
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Wang B, Ye K. Nop9 binds the central pseudoknot region of 18S rRNA. Nucleic Acids Res 2017; 45:3559-3567. [PMID: 28053123 PMCID: PMC5389560 DOI: 10.1093/nar/gkw1323] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/05/2016] [Accepted: 12/19/2016] [Indexed: 01/21/2023] Open
Abstract
The assembly of eukaryotic ribosomes requires numerous factors that transiently associate with evolving pre-ribosomal particles. The Pumilio repeat-containing protein Nop9 briefly associates with the 90S pre-ribosome during its co-transcriptional assembly. Here, we show that Nop9 specifically binds an 11-nucleotide sequence of 18S rRNA that forms the 3΄ side of the central pseudoknot and helix 28 in the mature subunit. Crystal structures of Nop9 in the free and RNA-bound states reveal a new type of Pumilio repeat protein with a distinct structure, target sequence and RNA-binding mode. Nop9 contains 10 Pumilio repeats arranged into a U-shaped scaffold. The target RNA is recognized by two stretches of repeats in a bipartite manner, and three central bases are unrecognized as a result of the degeneracy of repeats 6 and 7. Our data suggest that Nop9 regulates the folding of 18S rRNA at early assembly stages of 90S.
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Affiliation(s)
- Bing Wang
- Department of Biochemistry and Molecular Biology, College of Life Sciences, Beijing Normal University, Beijing 100875, China.,National Institute of Biological Sciences, Beijing 102206, China.,Key Laboratory of RNA Biology, CAS Center for Excellence in Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing 100101, China
| | - Keqiong Ye
- Key Laboratory of RNA Biology, CAS Center for Excellence in Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing 100101, China.,University of Chinese Academy of Sciences, Beijing 100049, China
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73
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Kressler D, Hurt E, Baßler J. A Puzzle of Life: Crafting Ribosomal Subunits. Trends Biochem Sci 2017; 42:640-654. [DOI: 10.1016/j.tibs.2017.05.005] [Citation(s) in RCA: 95] [Impact Index Per Article: 13.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2017] [Revised: 03/16/2017] [Accepted: 05/05/2017] [Indexed: 01/24/2023]
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74
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Zinder JC, Lima CD. Targeting RNA for processing or destruction by the eukaryotic RNA exosome and its cofactors. Genes Dev 2017; 31:88-100. [PMID: 28202538 PMCID: PMC5322736 DOI: 10.1101/gad.294769.116] [Citation(s) in RCA: 151] [Impact Index Per Article: 21.6] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
In this review, Zinder and Lima highlight recent advances that have illuminated roles for the RNA exosome and its cofactors in specific biological pathways, alongside studies that attempted to dissect these activities through structural and biochemical characterization of nuclear and cytoplasmic RNA exosome complexes. The eukaryotic RNA exosome is an essential and conserved protein complex that can degrade or process RNA substrates in the 3′-to-5′ direction. Since its discovery nearly two decades ago, studies have focused on determining how the exosome, along with associated cofactors, achieves the demanding task of targeting particular RNAs for degradation and/or processing in both the nucleus and cytoplasm. In this review, we highlight recent advances that have illuminated roles for the RNA exosome and its cofactors in specific biological pathways, alongside studies that attempted to dissect these activities through structural and biochemical characterization of nuclear and cytoplasmic RNA exosome complexes.
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Affiliation(s)
- John C Zinder
- Tri-Institutional Training Program in Chemical Biology, Memorial Sloan Kettering Cancer Center, New York, New York 10065, USA.,Structural Biology Program, Sloan Kettering Institute, New York, New York, 10065, USA
| | - Christopher D Lima
- Structural Biology Program, Sloan Kettering Institute, New York, New York, 10065, USA.,Howard Hughes Medical Institute, New York, New York, 10065 USA
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75
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Boissier F, Schmidt CM, Linnemann J, Fribourg S, Perez-Fernandez J. Pwp2 mediates UTP-B assembly via two structurally independent domains. Sci Rep 2017; 7:3169. [PMID: 28600509 PMCID: PMC5466602 DOI: 10.1038/s41598-017-03034-y] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/03/2017] [Accepted: 04/21/2017] [Indexed: 11/24/2022] Open
Abstract
The SSU processome constitutes a large ribonucleoprotein complex involved in the early steps of ribosome biogenesis. UTP-B is one of the first multi-subunit protein complexes that associates with the pre-ribosomal RNA to form the SSU processome. To understand the molecular basis of the hierarchical assembly of the SSU-processome, we have undergone a structural and functional analysis of the UTP-B subunit Pwp2p. We show that Pwp2p is required for the proper assembly of UTP-B and for a productive association of UTP-B with pre-rRNA. These two functions are mediated by two distinct structural domains. The N-terminal domain of Pwp2p folds into a tandem WD-repeat (tWD) that associates with Utp21p, Utp18p, and Utp6p to form a core complex. The CTDs of Pwp2p and Utp21p mediate the assembly of the heterodimer Utp12p:Utp13p that is required for the stable incorporation of the UTP-B complex in the SSU processome. Finally, we provide evidence suggesting a role of UTP-B as a platform for the binding of assembly factors during the maturation of 20S rRNA precursors.
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Affiliation(s)
- Fanny Boissier
- Université de Bordeaux, INSERM U1212, CNRS 5320, Bordeaux, France
| | - Christina Maria Schmidt
- Universität Regensburg, Biochemie-Zentrum Regensburg (BZR), Lehrstuhl Biochemie III, D-93053, Regensburg, Germany
| | - Jan Linnemann
- Universität Regensburg, Biochemie-Zentrum Regensburg (BZR), Lehrstuhl Biochemie III, D-93053, Regensburg, Germany
| | | | - Jorge Perez-Fernandez
- Universität Regensburg, Biochemie-Zentrum Regensburg (BZR), Lehrstuhl Biochemie III, D-93053, Regensburg, Germany.
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76
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Sharma S, Yang J, van Nues R, Watzinger P, Kötter P, Lafontaine DLJ, Granneman S, Entian KD. Specialized box C/D snoRNPs act as antisense guides to target RNA base acetylation. PLoS Genet 2017; 13:e1006804. [PMID: 28542199 PMCID: PMC5464676 DOI: 10.1371/journal.pgen.1006804] [Citation(s) in RCA: 79] [Impact Index Per Article: 11.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/14/2016] [Revised: 06/08/2017] [Accepted: 05/05/2017] [Indexed: 12/19/2022] Open
Abstract
Box C/D snoRNAs are known to guide site-specific ribose methylation of ribosomal RNA. Here, we demonstrate a novel and unexpected role for box C/D snoRNAs in guiding 18S rRNA acetylation in yeast. Our results demonstrate, for the first time, that the acetylation of two cytosine residues in 18S rRNA catalyzed by Kre33 is guided by two orphan box C/D snoRNAs-snR4 and snR45 -not known to be involved in methylation in yeast. We identified Kre33 binding sites on these snoRNAs as well as on the 18S rRNA, and demonstrate that both snR4 and snR45 establish extended bipartite complementarity around the cytosines targeted for acetylation, similar to pseudouridylation pocket formation by the H/ACA snoRNPs. We show that base pairing between these snoRNAs and 18S rRNA requires the putative helicase activity of Kre33, which is also needed to aid early pre-rRNA processing. Compared to yeast, the number of orphan box C/D snoRNAs in higher eukaryotes is much larger and we hypothesize that several of these may be involved in base-modifications.
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Affiliation(s)
- Sunny Sharma
- Institute of Molecular Biosciences, Goethe University, Frankfurt am Main, Germany
- RNA Molecular Biology and CMMI, F.R.S./FNRS and Université Libre de Bruxelles Rue Profs Jeener & Brachet, Charleroi–Gosselies, Belgium
| | - Jun Yang
- Institute of Molecular Biosciences, Goethe University, Frankfurt am Main, Germany
| | - Rob van Nues
- Institute of Structural and Molecular Biology, Centre for Synthetic and Systems Biology (SynthSys), University of Edinburgh, Edinburgh, United Kingdom
- Institute of Cell Biology, University of Edinburgh, Edinburgh, United Kingdom
| | - Peter Watzinger
- Institute of Molecular Biosciences, Goethe University, Frankfurt am Main, Germany
| | - Peter Kötter
- Institute of Molecular Biosciences, Goethe University, Frankfurt am Main, Germany
| | - Denis L. J. Lafontaine
- RNA Molecular Biology and CMMI, F.R.S./FNRS and Université Libre de Bruxelles Rue Profs Jeener & Brachet, Charleroi–Gosselies, Belgium
| | - Sander Granneman
- Institute of Structural and Molecular Biology, Centre for Synthetic and Systems Biology (SynthSys), University of Edinburgh, Edinburgh, United Kingdom
| | - Karl-Dieter Entian
- Institute of Molecular Biosciences, Goethe University, Frankfurt am Main, Germany
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77
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Espinar-Marchena FJ, Babiano R, Cruz J. Placeholder factors in ribosome biogenesis: please, pave my way. MICROBIAL CELL 2017; 4:144-168. [PMID: 28685141 PMCID: PMC5425277 DOI: 10.15698/mic2017.05.572] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 01/23/2023]
Abstract
The synthesis of cytoplasmic eukaryotic ribosomes is an extraordinarily energy-demanding cellular activity that occurs progressively from the nucleolus to the cytoplasm. In the nucleolus, precursor rRNAs associate with a myriad of trans-acting factors and some ribosomal proteins to form pre-ribosomal particles. These factors include snoRNPs, nucleases, ATPases, GTPases, RNA helicases, and a vast list of proteins with no predicted enzymatic activity. Their coordinate activity orchestrates in a spatiotemporal manner the modification and processing of precursor rRNAs, the rearrangement reactions required for the formation of productive RNA folding intermediates, the ordered assembly of the ribosomal proteins, and the export of pre-ribosomal particles to the cytoplasm; thus, providing speed, directionality and accuracy to the overall process of formation of translation-competent ribosomes. Here, we review a particular class of trans-acting factors known as "placeholders". Placeholder factors temporarily bind selected ribosomal sites until these have achieved a structural context that is appropriate for exchanging the placeholder with another site-specific binding factor. By this strategy, placeholders sterically prevent premature recruitment of subsequently binding factors, premature formation of structures, avoid possible folding traps, and act as molecular clocks that supervise the correct progression of pre-ribosomal particles into functional ribosomal subunits. We summarize the current understanding of those factors that delay the assembly of distinct ribosomal proteins or subsequently bind key sites in pre-ribosomal particles. We also discuss recurrent examples of RNA-protein and protein-protein mimicry between rRNAs and/or factors, which have clear functional implications for the ribosome biogenesis pathway.
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Affiliation(s)
- Francisco J Espinar-Marchena
- Instituto de Biomedicina de Sevilla (IBiS), Hospital Universitario Virgen del Rocío/CSIC/Universidad de Sevilla, and Departamento de Genética, Universidad de Sevilla, E-41013, Seville, Spain
| | - Reyes Babiano
- Instituto de Biomedicina de Sevilla (IBiS), Hospital Universitario Virgen del Rocío/CSIC/Universidad de Sevilla, and Departamento de Genética, Universidad de Sevilla, E-41013, Seville, Spain.,Instituto de Biomedicina de Sevilla (IBiS), Hospital Universitario Virgen del Rocío/CSIC/Universidad de Sevilla, and Departamento de Genética, Universidad de Sevilla, E-41013, Seville, Spain
| | - Jesús Cruz
- Instituto de Biomedicina de Sevilla (IBiS), Hospital Universitario Virgen del Rocío/CSIC/Universidad de Sevilla, and Departamento de Genética, Universidad de Sevilla, E-41013, Seville, Spain
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78
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Sun Q, Zhu X, Qi J, An W, Lan P, Tan D, Chen R, Wang B, Zheng S, Zhang C, Chen X, Zhang W, Chen J, Dong MQ, Ye K. Molecular architecture of the 90S small subunit pre-ribosome. eLife 2017; 6. [PMID: 28244370 PMCID: PMC5354517 DOI: 10.7554/elife.22086] [Citation(s) in RCA: 104] [Impact Index Per Article: 14.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/07/2016] [Accepted: 02/26/2017] [Indexed: 12/12/2022] Open
Abstract
Eukaryotic small ribosomal subunits are first assembled into 90S pre-ribosomes. The complete 90S is a gigantic complex with a molecular mass of approximately five megadaltons. Here, we report the nearly complete architecture of Saccharomyces cerevisiae 90S determined from three cryo-electron microscopy single particle reconstructions at 4.5 to 8.7 angstrom resolution. The majority of the density maps were modeled and assigned to specific RNA and protein components. The nascent ribosome is assembled into isolated native-like substructures that are stabilized by abundant assembly factors. The 5' external transcribed spacer and U3 snoRNA nucleate a large subcomplex that scaffolds the nascent ribosome. U3 binds four sites of pre-rRNA, including a novel site on helix 27 but not the 3' side of the central pseudoknot, and crucially organizes the 90S structure. The 90S model provides significant insight into the principle of small subunit assembly and the function of assembly factors. DOI:http://dx.doi.org/10.7554/eLife.22086.001
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Affiliation(s)
- Qi Sun
- PTN Joint Graduate Program, School of Life Sciences, Tsinghua University, Beijing, China.,Key Laboratory of RNA Biology, Institute of Biophysics, CAS Center for Excellence in Biomacromolecules, Chinese Academy of Sciences, Beijing, China.,National Institute of Biological Sciences, Beijing, China
| | - Xing Zhu
- Key Laboratory of RNA Biology, Institute of Biophysics, CAS Center for Excellence in Biomacromolecules, Chinese Academy of Sciences, Beijing, China
| | - Jia Qi
- Key Laboratory of RNA Biology, Institute of Biophysics, CAS Center for Excellence in Biomacromolecules, Chinese Academy of Sciences, Beijing, China.,National Institute of Biological Sciences, Beijing, China.,Department of Biochemistry and Molecular Biology, College of Life Sciences, Beijing Normal University, Beijing, China
| | - Weidong An
- Key Laboratory of RNA Biology, Institute of Biophysics, CAS Center for Excellence in Biomacromolecules, Chinese Academy of Sciences, Beijing, China.,National Institute of Biological Sciences, Beijing, China.,College of Biological Sciences, China Agricultural University, Beijing, China
| | - Pengfei Lan
- National Institute of Biological Sciences, Beijing, China
| | - Dan Tan
- National Institute of Biological Sciences, Beijing, China
| | - Rongchang Chen
- Key Laboratory of RNA Biology, Institute of Biophysics, CAS Center for Excellence in Biomacromolecules, Chinese Academy of Sciences, Beijing, China
| | - Bing Wang
- Key Laboratory of RNA Biology, Institute of Biophysics, CAS Center for Excellence in Biomacromolecules, Chinese Academy of Sciences, Beijing, China.,National Institute of Biological Sciences, Beijing, China
| | - Sanduo Zheng
- National Institute of Biological Sciences, Beijing, China
| | - Cheng Zhang
- National Institute of Biological Sciences, Beijing, China
| | - Xining Chen
- National Institute of Biological Sciences, Beijing, China
| | - Wei Zhang
- National Institute of Biological Sciences, Beijing, China
| | - Jing Chen
- PTN Joint Graduate Program, School of Life Sciences, Tsinghua University, Beijing, China.,Key Laboratory of RNA Biology, Institute of Biophysics, CAS Center for Excellence in Biomacromolecules, Chinese Academy of Sciences, Beijing, China.,National Institute of Biological Sciences, Beijing, China
| | - Meng-Qiu Dong
- National Institute of Biological Sciences, Beijing, China
| | - Keqiong Ye
- Key Laboratory of RNA Biology, Institute of Biophysics, CAS Center for Excellence in Biomacromolecules, Chinese Academy of Sciences, Beijing, China.,University of Chinese Academy of Sciences, Beijing, China
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79
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Architecture of the 90S Pre-ribosome: A Structural View on the Birth of the Eukaryotic Ribosome. Cell 2017; 166:380-393. [PMID: 27419870 DOI: 10.1016/j.cell.2016.06.014] [Citation(s) in RCA: 158] [Impact Index Per Article: 22.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/26/2016] [Revised: 04/05/2016] [Accepted: 06/01/2016] [Indexed: 12/13/2022]
Abstract
The 90S pre-ribosome is an early biogenesis intermediate formed during co-transcriptional ribosome formation, composed of ∼70 assembly factors and several small nucleolar RNAs (snoRNAs) that associate with nascent pre-rRNA. We report the cryo-EM structure of the Chaetomium thermophilum 90S pre-ribosome, revealing how a network of biogenesis factors including 19 β-propellers and large α-solenoid proteins engulfs the pre-rRNA. Within the 90S pre-ribosome, we identify the UTP-A, UTP-B, Mpp10-Imp3-Imp4, Bms1-Rcl1, and U3 snoRNP modules, which are organized around 5'-ETS and partially folded 18S rRNA. The U3 snoRNP is strategically positioned at the center of the 90S particle to perform its multiple tasks during pre-rRNA folding and processing. The architecture of the elusive 90S pre-ribosome gives unprecedented structural insight into the early steps of pre-rRNA maturation. Nascent rRNA that is co-transcriptionally folded and given a particular shape by encapsulation within a dedicated mold-like structure is reminiscent of how polypeptides use chaperone chambers for their protein folding.
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80
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Chaker-Margot M, Barandun J, Hunziker M, Klinge S. Architecture of the yeast small subunit processome. Science 2016; 355:science.aal1880. [PMID: 27980088 DOI: 10.1126/science.aal1880] [Citation(s) in RCA: 99] [Impact Index Per Article: 12.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/12/2016] [Accepted: 12/05/2016] [Indexed: 12/21/2022]
Abstract
The small subunit (SSU) processome, a large ribonucleoprotein particle, organizes the assembly of the eukaryotic small ribosomal subunit by coordinating the folding, cleavage, and modification of nascent pre-ribosomal RNA (rRNA). Here, we present the cryo-electron microscopy structure of the yeast SSU processome at 5.1-angstrom resolution. The structure reveals how large ribosome biogenesis complexes assist the 5' external transcribed spacer and U3 small nucleolar RNA in providing an intertwined RNA-protein assembly platform for the separate maturation of 18S rRNA domains. The strategic placement of a molecular motor at the center of the particle further suggests a mechanism for mediating conformational changes within this giant particle. This study provides a structural framework for a mechanistic understanding of eukaryotic ribosome assembly in the model organism Saccharomyces cerevisiae.
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Affiliation(s)
- Malik Chaker-Margot
- Laboratory of Protein and Nucleic Acid Chemistry, The Rockefeller University, New York, NY 10065, USA.,Tri-Institutional Training Program in Chemical Biology, The Rockefeller University, New York, NY 10065, USA
| | - Jonas Barandun
- Laboratory of Protein and Nucleic Acid Chemistry, The Rockefeller University, New York, NY 10065, USA
| | - Mirjam Hunziker
- Laboratory of Protein and Nucleic Acid Chemistry, The Rockefeller University, New York, NY 10065, USA
| | - Sebastian Klinge
- Laboratory of Protein and Nucleic Acid Chemistry, The Rockefeller University, New York, NY 10065, USA.
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81
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Greber BJ. Mechanistic insight into eukaryotic 60S ribosomal subunit biogenesis by cryo-electron microscopy. RNA (NEW YORK, N.Y.) 2016; 22:1643-1662. [PMID: 27875256 PMCID: PMC5066618 DOI: 10.1261/rna.057927.116] [Citation(s) in RCA: 39] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/08/2023]
Abstract
Eukaryotic ribosomes, the protein-producing factories of the cell, are composed of four ribosomal RNA molecules and roughly 80 proteins. Their biogenesis is a complex process that involves more than 200 biogenesis factors that facilitate the production, modification, and assembly of ribosomal components and the structural transitions along the maturation pathways of the pre-ribosomal particles. Here, I review recent structural and mechanistic insights into the biogenesis of the large ribosomal subunit that were furthered by cryo-electron microscopy of natively purified pre-60S particles and in vitro reconstituted ribosome assembly factor complexes. Combined with biochemical, genetic, and previous structural data, these structures have provided detailed insights into the assembly and maturation of the central protuberance of the 60S subunit, the network of biogenesis factors near the ribosomal tunnel exit, and the functional activation of the large ribosomal subunit during cytoplasmic maturation.
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Affiliation(s)
- Basil J Greber
- California Institute for Quantitative Biosciences (QB3), University of California, Berkeley, California 94720-3220, USA
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82
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Zhang J, McCann KL, Qiu C, Gonzalez LE, Baserga SJ, Hall TMT. Nop9 is a PUF-like protein that prevents premature cleavage to correctly process pre-18S rRNA. Nat Commun 2016; 7:13085. [PMID: 27725644 PMCID: PMC5062617 DOI: 10.1038/ncomms13085] [Citation(s) in RCA: 28] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/10/2015] [Accepted: 09/01/2016] [Indexed: 12/16/2022] Open
Abstract
Numerous factors direct eukaryotic ribosome biogenesis, and defects in a single ribosome assembly factor may be lethal or produce tissue-specific human ribosomopathies. Pre-ribosomal RNAs (pre-rRNAs) must be processed stepwise and at the correct subcellular locations to produce the mature rRNAs. Nop9 is a conserved small ribosomal subunit biogenesis factor, essential in yeast. Here we report a 2.1-Å crystal structure of Nop9 and a small-angle X-ray-scattering model of a Nop9:RNA complex that reveals a ‘C'-shaped fold formed from 11 Pumilio repeats. We show that Nop9 recognizes sequence and structural features of the 20S pre-rRNA near the cleavage site of the nuclease, Nob1. We further demonstrate that Nop9 inhibits Nob1 cleavage, the final processing step to produce mature small ribosomal subunit 18S rRNA. Together, our results suggest that Nop9 is critical for timely cleavage of the 20S pre-rRNA. Moreover, the Nop9 structure exemplifies a new class of Pumilio repeat proteins. Nop9 is a conserved small ribosomal subunit biogenesis factor. Here, Zhang et al. show that Nop9, in complex with RNA, adopts a C-shaped fold formed from 11 Pumillo repeats and propose that Nop9 inhibits premature cleavage of 20S pre-rRNA by inhibiting the Nob1 nuclease.
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Affiliation(s)
- Jun Zhang
- Epigenetics and Stem Cell Biology Laboratory, National Institute of Environmental Health Sciences, National Institutes of Health, PO Box 12233, MD F3-05, Research Triangle Park, North Carolina 27709, USA
| | - Kathleen L McCann
- Epigenetics and Stem Cell Biology Laboratory, National Institute of Environmental Health Sciences, National Institutes of Health, PO Box 12233, MD F3-05, Research Triangle Park, North Carolina 27709, USA.,Department of Genetics, Yale University School of Medicine, New Haven, Connecticut 06520, USA
| | - Chen Qiu
- Epigenetics and Stem Cell Biology Laboratory, National Institute of Environmental Health Sciences, National Institutes of Health, PO Box 12233, MD F3-05, Research Triangle Park, North Carolina 27709, USA
| | - Lauren E Gonzalez
- Epigenetics and Stem Cell Biology Laboratory, National Institute of Environmental Health Sciences, National Institutes of Health, PO Box 12233, MD F3-05, Research Triangle Park, North Carolina 27709, USA
| | - Susan J Baserga
- Department of Genetics, Yale University School of Medicine, New Haven, Connecticut 06520, USA.,Department of Therapeutic Radiology, Yale University School of Medicine, New Haven, Connecticut 06520, USA.,Department of Molecular Biophysics and Biochemistry, Yale University School of Medicine, New Haven, Connecticut 06520, USA
| | - Traci M Tanaka Hall
- Epigenetics and Stem Cell Biology Laboratory, National Institute of Environmental Health Sciences, National Institutes of Health, PO Box 12233, MD F3-05, Research Triangle Park, North Carolina 27709, USA
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83
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Abstract
Box C/D RNAs guide site-specific 2'-O-methylation of RNAs in archaea and eukaryotes. The spacer regions between boxes C to D' and boxes C' to D contain the guide sequence that can form a stretch of base pairs with substrate RNAs. The lengths of spacer regions and guide-substrate duplexes are variable among C/D RNAs. In a previously determined structure of C/D ribonucleoprotein (RNP), a 12-nt-long spacer forms 10 bp with the substrate. How spacers and guide-substrate duplexes of other lengths are accommodated remains unknown. Here we analyze how the lengths of spacers and guide-substrate duplexes affect the modification activity and determine three structures of C/D RNPs assembled with different spacers and substrates. We show that the guide can only form a duplex of a maximum of 10 bp with the substrate during modification. Slightly shorter duplexes are tolerated, but longer duplexes must be unwound to fit into a capped protein channel for modification. Spacers with <12 nucleotides are defective, mainly because they cannot load the substrate in the active conformation. For spacers with >12 nucleotides, the excessive unpaired sequences near the box C/C' side are looped out. Our results provide insight into the substrate recognition mechanism of C/D RNA and refute the RNA-swapped model for dimeric C/D RNP.
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Affiliation(s)
- Zuxiao Yang
- College of Biological Sciences, China Agricultural University, Beijing 100193, China; National Institute of Biological Sciences, Beijing 102206, China; Key Laboratory of RNA Biology, CAS Center for Excellence in Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing 100101, China; Beijing Key Laboratory of Noncoding RNA, Institute of Biophysics, Chinese Academy of Sciences, Beijing 100101, China
| | - Jinzhong Lin
- National Institute of Biological Sciences, Beijing 102206, China
| | - Keqiong Ye
- Key Laboratory of RNA Biology, CAS Center for Excellence in Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing 100101, China; Beijing Key Laboratory of Noncoding RNA, Institute of Biophysics, Chinese Academy of Sciences, Beijing 100101, China; University of Chinese Academy of Sciences, Beijing 100049, China
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84
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85
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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 2016; 30:718-32. [PMID: 26980190 PMCID: PMC4803056 DOI: 10.1101/gad.274688.115] [Citation(s) in RCA: 88] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Abstract
In this study, Zhang et al. researched how the 90S preribosomal particle is cotranscriptionally assembled in yeast using a novel approach. They determined the assembly point of 65 proteins and the U3, U14, and snR30 snoRNAs, revealing a stepwise and dynamic assembly map, thereby advancing our understanding of small subunit biogenesis. The eukaryotic ribosomal RNA (rRNA) is associated cotranscriptionally with numerous factors into an enormous 90S preribosomal particle that conducts early processing of small ribosomal subunits. The assembly pathway and structure of the 90S particle is poorly understood. Here, we affinity-purified and analyzed the constituents of yeast 90S particles that were assembled on a series of plasmid-encoded 3′-truncated pre-18S RNAs. We determined the assembly point of 65 proteins and the U3, U14, and snR30 small nucleolar RNAs (snoRNAs), revealing a stepwise and dynamic assembly map. The 5′ external transcribed spacer (ETS) alone can nucleate a large complex. When the 18S rRNA is nearly complete, the 90S structure undergoes a dramatic reorganization, releasing U14, snR30, and 14 protein factors that bind earlier. We also identified a reference state of 90S that is fully assembled yet has not undergone 5′ETS processing. The assembly map present here provides a new framework to understand small subunit biogenesis.
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Affiliation(s)
- Liman Zhang
- National Institute of Biological Sciences, Beijing, Beijing 102206, China
| | - Chen Wu
- National Institute of Biological Sciences, Beijing, Beijing 102206, China; College of Biological Sciences, China Agricultural University, Beijing 100193, China; Key Laboratory of RNA Biology, Institute of Biophysics, Chinese Academy of Sciences, Beijing 100101, China; Beijing Key Laboratory of Noncoding RNA, Institute of Biophysics, Chinese Academy of Sciences, Beijing 100101, China
| | - Gaihong Cai
- National Institute of Biological Sciences, Beijing, Beijing 102206, China
| | - She Chen
- National Institute of Biological Sciences, Beijing, Beijing 102206, China
| | - Keqiong Ye
- Key Laboratory of RNA Biology, Institute of Biophysics, Chinese Academy of Sciences, Beijing 100101, China; Beijing Key Laboratory of Noncoding RNA, Institute of Biophysics, Chinese Academy of Sciences, Beijing 100101, China
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86
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Abstract
Many proteins have been implicated genetically and biochemically in the assembly of eukaryotic ribosomes. Now, Kornprobst et al. show us how they are put together with a cryoEM structure of the 90S processome that initiates ribosome assembly, revealing the arrangement of U3 RNA and the several UTP complexes that form a chaperone-like structure around and within the developing 40S ribosomal subunit.
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Affiliation(s)
- Jonathan R Warner
- Department of Cell Biology, Albert Einstein College of Medicine, Bronx, NY 10461, USA.
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87
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Hunziker M, Barandun J, Petfalski E, Tan D, Delan-Forino C, Molloy KR, Kim KH, Dunn-Davies H, Shi Y, Chaker-Margot M, Chait BT, Walz T, Tollervey D, Klinge S. UtpA and UtpB chaperone nascent pre-ribosomal RNA and U3 snoRNA to initiate eukaryotic ribosome assembly. Nat Commun 2016; 7:12090. [PMID: 27354316 PMCID: PMC4931317 DOI: 10.1038/ncomms12090] [Citation(s) in RCA: 56] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/06/2016] [Accepted: 05/27/2016] [Indexed: 01/14/2023] Open
Abstract
Early eukaryotic ribosome biogenesis involves large multi-protein complexes, which co-transcriptionally associate with pre-ribosomal RNA to form the small subunit processome. The precise mechanisms by which two of the largest multi-protein complexes—UtpA and UtpB—interact with nascent pre-ribosomal RNA are poorly understood. Here, we combined biochemical and structural biology approaches with ensembles of RNA–protein cross-linking data to elucidate the essential functions of both complexes. We show that UtpA contains a large composite RNA-binding site and captures the 5′ end of pre-ribosomal RNA. UtpB forms an extended structure that binds early pre-ribosomal intermediates in close proximity to architectural sites such as an RNA duplex formed by the 5′ ETS and U3 snoRNA as well as the 3′ boundary of the 18S rRNA. Both complexes therefore act as vital RNA chaperones to initiate eukaryotic ribosome assembly. Eukaryotic ribosome biogenesis involves a large number of maturations factors which are responsible for the stepwise assembly of the ribosomal subunits. Here the authors use an array of biochemical and structural biology methods to investigate the function of the UtpA and UtpB complexes as part of the small subunit processome.
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Affiliation(s)
- Mirjam Hunziker
- Laboratory of Protein and Nucleic Acid Chemistry, The Rockefeller University, New York, New York 10065, USA
| | - Jonas Barandun
- Laboratory of Protein and Nucleic Acid Chemistry, The Rockefeller University, New York, New York 10065, USA
| | - Elisabeth Petfalski
- Wellcome Trust Centre for Cell Biology, University of Edinburgh, Michael Swann Building, Max Born Crescent, Edinburgh EH9 3BF, UK
| | - Dongyan Tan
- Department of Cell Biology, Harvard Medical School, Boston, Massachusetts 02115, USA
| | - Clémentine Delan-Forino
- Wellcome Trust Centre for Cell Biology, University of Edinburgh, Michael Swann Building, Max Born Crescent, Edinburgh EH9 3BF, UK
| | - Kelly R Molloy
- Laboratory of Mass Spectrometry and Gaseous Ion Chemistry, The Rockefeller University, New York, New York 10065, USA
| | - Kelly H Kim
- Laboratory of Molecular Electron Microscopy, The Rockefeller University, New York, New York 10065, USA
| | - Hywel Dunn-Davies
- Wellcome Trust Centre for Cell Biology, University of Edinburgh, Michael Swann Building, Max Born Crescent, Edinburgh EH9 3BF, UK
| | - Yi Shi
- Laboratory of Mass Spectrometry and Gaseous Ion Chemistry, The Rockefeller University, New York, New York 10065, USA
| | - Malik Chaker-Margot
- Laboratory of Protein and Nucleic Acid Chemistry, The Rockefeller University, New York, New York 10065, USA.,Tri-Institutional Training Program in Chemical Biology, The Rockefeller University, New York, New York 10065, USA
| | - Brian T Chait
- Laboratory of Mass Spectrometry and Gaseous Ion Chemistry, The Rockefeller University, New York, New York 10065, USA
| | - Thomas Walz
- Laboratory of Molecular Electron Microscopy, The Rockefeller University, New York, New York 10065, USA
| | - David Tollervey
- Wellcome Trust Centre for Cell Biology, University of Edinburgh, Michael Swann Building, Max Born Crescent, Edinburgh EH9 3BF, UK
| | - Sebastian Klinge
- Laboratory of Protein and Nucleic Acid Chemistry, The Rockefeller University, New York, New York 10065, USA
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88
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Khoshnevis S, Askenasy I, Johnson MC, Dattolo MD, Young-Erdos CL, Stroupe ME, Karbstein K. The DEAD-box Protein Rok1 Orchestrates 40S and 60S Ribosome Assembly by Promoting the Release of Rrp5 from Pre-40S Ribosomes to Allow for 60S Maturation. PLoS Biol 2016; 14:e1002480. [PMID: 27280440 PMCID: PMC4900678 DOI: 10.1371/journal.pbio.1002480] [Citation(s) in RCA: 33] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/25/2016] [Accepted: 05/10/2016] [Indexed: 12/25/2022] Open
Abstract
DEAD-box proteins are ubiquitous regulators of RNA biology. While commonly dubbed “helicases,” their activities also include duplex annealing, adenosine triphosphate (ATP)-dependent RNA binding, and RNA-protein complex remodeling. Rok1, an essential DEAD-box protein, and its cofactor Rrp5 are required for ribosome assembly. Here, we use in vivo and in vitro biochemical analyses to demonstrate that ATP-bound Rok1, but not adenosine diphosphate (ADP)-bound Rok1, stabilizes Rrp5 binding to 40S ribosomes. Interconversion between these two forms by ATP hydrolysis is required for release of Rrp5 from pre-40S ribosomes in vivo, thereby allowing Rrp5 to carry out its role in 60S subunit assembly. Furthermore, our data also strongly suggest that the previously described accumulation of snR30 upon Rok1 inactivation arises because Rrp5 release is blocked and implicate a previously undescribed interaction between Rrp5 and the DEAD-box protein Has1 in mediating snR30 accumulation when Rrp5 release from pre-40S subunits is blocked. During ribosomal biogenesis, Rrp5 is unusual in being required for assembly of both small and large subunits. This study demonstrates a role for ATP hydrolysis by the DEAD-box protein Rok1 in releasing Rrp5 from pre-40S subunits. Assembly of the small and large ribosomal subunits requires two separate machineries. The assembly factor Rrp5 is unusual in being one of only three proteins required for assembly of both subunits. While it binds cotranscriptionally during early stages of small subunit assembly, it departs with large subunit intermediates after the separation of these precursors. How Rrp5 switches from interacting with small subunit precursors to binding large subunit precursors remains unknown but is potentially important, as it could regulate the interplay between small and large subunit assembly. Here, we show that the DEAD-box protein Rok1, a member of a ubiquitous class of RNA-dependent ATPases, releases Rrp5 from assembling small subunits to allow for its function in large subunit assembly. We show that a complex of Rrp5, Rok1, and adenosine triphosphate (ATP) binds small subunits or mimics of ribosomal RNA more tightly than does a complex of Rrp5, Rok1, and adenosine diphosphate (ADP). In cells, interconversion between the ATP and the ADP-form of Rok1 is required for release of Rrp5 from nascent small subunits and for binding to assembling large subunits. Furthermore, we show that the release of snR30, which leads to formation of a large substructure on small subunits, also requires Rok1-mediated release of Rrp5.
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MESH Headings
- Adenosine Diphosphate/metabolism
- Adenosine Triphosphate/metabolism
- Binding Sites/genetics
- DEAD-box RNA Helicases/chemistry
- DEAD-box RNA Helicases/genetics
- DEAD-box RNA Helicases/metabolism
- Hydrolysis
- Models, Molecular
- Molecular Conformation
- Nuclear Proteins/chemistry
- Nuclear Proteins/genetics
- Nuclear Proteins/metabolism
- Protein Binding
- Protein Domains
- RNA, Fungal/chemistry
- RNA, Fungal/genetics
- RNA, Fungal/metabolism
- RNA, Small Nucleolar/chemistry
- RNA, Small Nucleolar/genetics
- RNA, Small Nucleolar/metabolism
- RNA-Binding Proteins/chemistry
- RNA-Binding Proteins/genetics
- RNA-Binding Proteins/metabolism
- Ribosome Subunits, Large, Eukaryotic/chemistry
- Ribosome Subunits, Large, Eukaryotic/genetics
- Ribosome Subunits, Large, Eukaryotic/metabolism
- Ribosome Subunits, Small, Eukaryotic/chemistry
- Ribosome Subunits, Small, Eukaryotic/genetics
- Ribosome Subunits, Small, Eukaryotic/metabolism
- Saccharomyces cerevisiae/genetics
- Saccharomyces cerevisiae/metabolism
- Saccharomyces cerevisiae Proteins/chemistry
- Saccharomyces cerevisiae Proteins/genetics
- Saccharomyces cerevisiae Proteins/metabolism
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Affiliation(s)
- Sohail Khoshnevis
- Department of Cancer Biology, The Scripps Research Institute, Jupiter, Florida, United States of America
| | - Isabel Askenasy
- Department of Biological Science and the Institute of Molecular Biophysics, Florida State University, Tallahassee, Florida, United States of America
| | - Matthew C. Johnson
- Department of Biological Science and the Institute of Molecular Biophysics, Florida State University, Tallahassee, Florida, United States of America
| | - Maria D. Dattolo
- Department of Cancer Biology, The Scripps Research Institute, Jupiter, Florida, United States of America
- The Benjamin School, Palm Beach Gardens, Florida, United States of America
| | - Crystal L. Young-Erdos
- Department of Cancer Biology, The Scripps Research Institute, Jupiter, Florida, United States of America
| | - M. Elizabeth Stroupe
- Department of Biological Science and the Institute of Molecular Biophysics, Florida State University, Tallahassee, Florida, United States of America
- * E-mail: (MES); (KK)
| | - Katrin Karbstein
- Department of Cancer Biology, The Scripps Research Institute, Jupiter, Florida, United States of America
- * E-mail: (MES); (KK)
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89
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Ribosomal 60S-subunit production: the final scene. Nat Struct Mol Biol 2015; 22:837-8. [DOI: 10.1038/nsmb.3121] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
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