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Mitterer V, Hamze H, Kunowska N, Stelzl U, Henras A, Hurt E. The RNA helicase Dbp10 coordinates assembly factor association with PTC maturation during ribosome biogenesis. Nucleic Acids Res 2024; 52:1975-1987. [PMID: 38113283 PMCID: PMC10899779 DOI: 10.1093/nar/gkad1206] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2023] [Revised: 11/08/2023] [Accepted: 12/11/2023] [Indexed: 12/21/2023] Open
Abstract
During ribosome biogenesis a plethora of assembly factors and essential enzymes drive the unidirectional maturation of nascent pre-ribosomal subunits. The DEAD-box RNA helicase Dbp10 is suggested to restructure pre-ribosomal rRNA of the evolving peptidyl-transferase center (PTC) on nucleolar ribosomal 60S assembly intermediates. Here, we show that point mutations within conserved catalytic helicase-core motifs of Dbp10 yield a dominant-lethal growth phenotype. Such dbp10 mutants, which stably associate with pre-60S intermediates, impair pre-60S biogenesis at a nucleolar stage prior to the release of assembly factor Rrp14 and stable integration of late nucleolar factors such as Noc3. Furthermore, the binding of the GTPase Nug1 to particles isolated directly via mutant Dbp10 bait proteins is specifically inhibited. The N-terminal domain of Nug1 interacts with Dbp10 and the methyltransferase Spb1, whose pre-60S incorporation is also reduced in absence of functional Dbp10 resulting in decreased methylation of 25S rRNA nucleotide G2922. Our data suggest that Dbp10's helicase activity generates the necessary framework for assembly factor docking thereby permitting PTC rRNA methylation and the progression of pre-60S maturation.
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Affiliation(s)
- Valentin Mitterer
- Biochemistry Center, University of Heidelberg, 69120 Heidelberg, Germany
- Institute of Molecular Biosciences, University of Graz, 8010 Graz, Austria
| | - Hussein Hamze
- Molecular, Cellular and Developmental Biology Unit (MCD), Center for Integrative Biology (CBI), CNRS, University of Toulouse, 31062 Toulouse, France
| | - Natalia Kunowska
- Institute of Pharmaceutical Sciences, Pharmaceutical Chemistry, University of Graz, 8010 Graz, Austria
| | - Ulrich Stelzl
- Institute of Pharmaceutical Sciences, Pharmaceutical Chemistry, University of Graz, 8010 Graz, Austria
- BioTechMed-Graz, 8010 Graz, Austria
- Field of Excellence BioHealth, University of Graz, 8010 Graz, Austria
| | - Anthony K Henras
- Molecular, Cellular and Developmental Biology Unit (MCD), Center for Integrative Biology (CBI), CNRS, University of Toulouse, 31062 Toulouse, France
| | - Ed Hurt
- Biochemistry Center, University of Heidelberg, 69120 Heidelberg, Germany
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2
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Musalgaonkar S, Yelland J, Chitale R, Rao S, Ozadam H, Cenik C, Taylor D, Johnson A. The Ribosome Assembly Factor Reh1 is Released from the Polypeptide Exit Tunnel in the Pioneer Round of Translation. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.10.23.563604. [PMID: 37961559 PMCID: PMC10634756 DOI: 10.1101/2023.10.23.563604] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/15/2023]
Abstract
Assembly of functional ribosomal subunits and successfully delivering them to the translating pool is a prerequisite for protein synthesis and cell growth. In S. cerevisiae, the ribosome assembly factor Reh1 binds to pre-60S subunits at a late stage during their cytoplasmic maturation. Previous work shows that the C-terminus of Reh1 inserts into the polypeptide exit tunnel (PET) of the pre-60S subunit. Unlike canonical assembly factors, which associate exclusively with pre-60S subunits, we observed that Reh1 sediments with polysomes in addition to free 60S subunits. We therefore investigated the intriguing possibility that Reh1 remains associated with 60S subunits after the release of the anti-association factor Tif6 and after subunit joining. Here, we show that Reh1-bound nascent 60S subunits associate with 40S subunits to form actively translating ribosomes. Using selective ribosome profiling, we found that Reh1-bound ribosomes populate open reading frames near start codons. Reh1-bound ribosomes are also strongly enriched for initiator tRNA, indicating they are associated with early elongation events. Using single particle cryo-electron microscopy to image cycloheximide-arrested Reh1-bound 80S ribosomes, we found that Reh1-bound 80S contain A site peptidyl tRNA, P site tRNA and eIF5A indicating that Reh1 does not dissociate from 60S until early stages of translation elongation. We propose that Reh1 is displaced by the elongating peptide chain. These results identify Reh1 as the last assembly factor released from the nascent 60S subunit during its pioneer round of translation.
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3
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Yelland JN, Bravo JPK, Black JJ, Taylor DW, Johnson AW. A single 2'-O-methylation of ribosomal RNA gates assembly of a functional ribosome. Nat Struct Mol Biol 2023; 30:91-98. [PMID: 36536102 PMCID: PMC9851907 DOI: 10.1038/s41594-022-00891-8] [Citation(s) in RCA: 9] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/07/2022] [Accepted: 11/04/2022] [Indexed: 12/24/2022]
Abstract
RNA modifications are widespread in biology and abundant in ribosomal RNA. However, the importance of these modifications is not well understood. We show that methylation of a single nucleotide, in the catalytic center of the large subunit, gates ribosome assembly. Massively parallel mutational scanning of the essential nuclear GTPase Nog2 identified important interactions with rRNA, particularly with the 2'-O-methylated A-site base Gm2922. We found that methylation of G2922 is needed for assembly and efficient nuclear export of the large subunit. Critically, we identified single amino acid changes in Nog2 that completely bypass dependence on G2922 methylation and used cryoelectron microscopy to directly visualize how methylation flips Gm2922 into the active site channel of Nog2. This work demonstrates that a single RNA modification is a critical checkpoint in ribosome biogenesis, suggesting that such modifications can play an important role in regulation and assembly of macromolecular machines.
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Affiliation(s)
- James N Yelland
- Interdisciplinary Life Sciences Graduate Program, University of Texas at Austin, Austin, TX, USA
| | - Jack P K Bravo
- Department of Molecular Biosciences, University of Texas at Austin, Austin, TX, USA
| | - Joshua J Black
- Department of Molecular Biosciences, University of Texas at Austin, Austin, TX, USA
- Department of Molecular Biology and Genetics, Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - David W Taylor
- Interdisciplinary Life Sciences Graduate Program, University of Texas at Austin, Austin, TX, USA.
- Department of Molecular Biosciences, University of Texas at Austin, Austin, TX, USA.
- Center for Systems and Synthetic Biology, University of Texas at Austin, Austin, TX, USA.
- Livestrong Cancer Institutes, Dell Medical School, Austin, TX, USA.
| | - Arlen W Johnson
- Interdisciplinary Life Sciences Graduate Program, University of Texas at Austin, Austin, TX, USA.
- Department of Molecular Biosciences, University of Texas at Austin, Austin, TX, USA.
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4
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Tseng YT, Sung YC, Liu CY, Lo KY. Translation initiation factor eIF4G1 modulates assembly of the polypeptide exit tunnel region in yeast ribosome biogenesis. J Cell Sci 2022; 135:275526. [PMID: 35615984 DOI: 10.1242/jcs.259540] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2021] [Accepted: 05/12/2022] [Indexed: 01/24/2023] Open
Abstract
eIF4G is an important eukaryotic translation initiation factor. In this study, eIF4G1, one of the eIF4G isoforms, was shown to directly participate in biogenesis of the large (60S) ribosomal subunit in Saccharomyces cerevisiae cells. Mutation of eIF4G1 decreased the amount 60S ribosomal subunits significantly. The C-terminal fragment of eIF4G1 could complement the function in 60S biogenesis. Analyses of its purified complex with mass spectrometry indicated that eIF4G1 associated with the pre-60S form directly. Strong genetic and direct protein-protein interactions were observed between eIF4G1 and Ssf1 protein. Upon deletion of eIF4G1, Ssf1, Rrp15, Rrp14 and Mak16 were abnormally retained on the pre-60S complex. This purturbed the loading of Arx1 and eL31 at the polypeptide exit tunnel (PET) site and the transition to a Nog2 complex. Our data indicate that eIF4G1 is important in facilitating PET maturation and 27S processing correctly. This article has an associated First Person interview with the first author of the paper.
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Affiliation(s)
- Yun-Ting Tseng
- Department of Agricultural Chemistry, College of Bioresources and Agriculture, National Taiwan University, Taipei 10617, Taiwan
| | - Yu-Cheng Sung
- Department of Agricultural Chemistry, College of Bioresources and Agriculture, National Taiwan University, Taipei 10617, Taiwan
| | - Ching-Yu Liu
- Department of Agricultural Chemistry, College of Bioresources and Agriculture, National Taiwan University, Taipei 10617, Taiwan
| | - Kai-Yin Lo
- Department of Agricultural Chemistry, College of Bioresources and Agriculture, National Taiwan University, Taipei 10617, Taiwan
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Three Small Cysteine-Free Proteins (CFP1–3) Are Required for Insect-Pathogenic Lifestyle of Metarhizium robertsii. J Fungi (Basel) 2022; 8:jof8060606. [PMID: 35736089 PMCID: PMC9224661 DOI: 10.3390/jof8060606] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2022] [Revised: 05/20/2022] [Accepted: 06/02/2022] [Indexed: 12/04/2022] Open
Abstract
Unique CFP (cysteine-free protein; 120 aa) has been identified as an extraordinary virulence factor in Beauveria bassiana (Cordycipitaceae), a main source of wide-spectrum fungal insecticides. Its homologs exclusively exist in wide-spectrum insect pathogens of Hypocreales, suggesting their importance for a fungal insect-pathogenic lifestyle. In this study, all three CFP homologs (CFP1–3, 128–145 aa) were proven essential virulence factors in Metarhizium robertsii (Clavicipitaceae). Despite limited effects on asexual cycles in vitro, knockout mutants of cfp1,cfp2 and cfp3 were severely compromised in their capability for normal cuticle infection, in which most tested Galleria mellonella larvae survived. The blocked cuticle infection concurred with reduced secretion of extracellular enzymes, including Pr1 proteases required cuticle penetration. Cuticle-bypassing infection by intrahemocoel injection of ~250 conidia per larva resulted in a greater reduction in virulence in the mutant of cfp1 (82%) than of cfp2 (21%) or cfp3 (25%) versus the parental wild-type. Transcriptomic analysis revealed dysregulation of 604 genes (up/down ratio: 251:353) in the Δcfp1 mutant. Many of them were involved in virulence-related cellular processes and events aside from 154 functionally unknown genes (up/down ratio: 56:98). These results reinforce the essential roles of small CFP homologs in hypocrealean fungal adaptation to insect-pathogenic lifestyle and their exploitability for the genetic improvement of fungal insecticidal activity.
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Oborská-Oplová M, Fischer U, Altvater M, Panse VG. Eukaryotic Ribosome assembly and Nucleocytoplasmic Transport. Methods Mol Biol 2022; 2533:99-126. [PMID: 35796985 PMCID: PMC9761919 DOI: 10.1007/978-1-0716-2501-9_7] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/15/2023]
Abstract
The process of eukaryotic ribosome assembly stretches across the nucleolus, the nucleoplasm and the cytoplasm, and therefore relies on efficient nucleocytoplasmic transport. In yeast, the import machinery delivers ~140,000 ribosomal proteins every minute to the nucleus for ribosome assembly. At the same time, the export machinery facilitates translocation of ~2000 pre-ribosomal particles every minute through ~200 nuclear pore complexes (NPC) into the cytoplasm. Eukaryotic ribosome assembly also requires >200 conserved assembly factors, which transiently associate with pre-ribosomal particles. Their site(s) of action on maturing pre-ribosomes are beginning to be elucidated. In this chapter, we outline protocols that enable rapid biochemical isolation of pre-ribosomal particles for single particle cryo-electron microscopy (cryo-EM) and in vitro reconstitution of nuclear transport processes. We discuss cell-biological and genetic approaches to investigate how the ribosome assembly and the nucleocytoplasmic transport machineries collaborate to produce functional ribosomes.
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Affiliation(s)
- Michaela Oborská-Oplová
- Institute of Biochemistry, ETH Zurich, Zurich, Switzerland
- Institute of Medical Microbiology, University of Zurich, Zurich, Switzerland
| | - Ute Fischer
- Institute of Biochemistry, ETH Zurich, Zurich, Switzerland
| | | | - Vikram Govind Panse
- Institute of Medical Microbiology, University of Zurich, Zurich, Switzerland.
- Faculty of Science, University of Zurich, Zurich, Switzerland.
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7
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Birikmen M, Bohnsack KE, Tran V, Somayaji S, Bohnsack MT, Ebersberger I. Tracing Eukaryotic Ribosome Biogenesis Factors Into the Archaeal Domain Sheds Light on the Evolution of Functional Complexity. Front Microbiol 2021; 12:739000. [PMID: 34603269 PMCID: PMC8481954 DOI: 10.3389/fmicb.2021.739000] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/09/2021] [Accepted: 08/17/2021] [Indexed: 01/23/2023] Open
Abstract
Ribosome assembly is an essential and carefully choreographed cellular process. In eukaryotes, several 100 proteins, distributed across the nucleolus, nucleus, and cytoplasm, co-ordinate the step-wise assembly of four ribosomal RNAs (rRNAs) and approximately 80 ribosomal proteins (RPs) into the mature ribosomal subunits. Due to the inherent complexity of the assembly process, functional studies identifying ribosome biogenesis factors and, more importantly, their precise functions and interplay are confined to a few and very well-established model organisms. Although best characterized in yeast (Saccharomyces cerevisiae), emerging links to disease and the discovery of additional layers of regulation have recently encouraged deeper analysis of the pathway in human cells. In archaea, ribosome biogenesis is less well-understood. However, their simpler sub-cellular structure should allow a less elaborated assembly procedure, potentially providing insights into the functional essentials of ribosome biogenesis that evolved long before the diversification of archaea and eukaryotes. Here, we use a comprehensive phylogenetic profiling setup, integrating targeted ortholog searches with automated scoring of protein domain architecture similarities and an assessment of when search sensitivity becomes limiting, to trace 301 curated eukaryotic ribosome biogenesis factors across 982 taxa spanning the tree of life and including 727 archaea. We show that both factor loss and lineage-specific modifications of factor function modulate ribosome biogenesis, and we highlight that limited sensitivity of the ortholog search can confound evolutionary conclusions. Projecting into the archaeal domain, we find that only few factors are consistently present across the analyzed taxa, and lineage-specific loss is common. While members of the Asgard group are not special with respect to their inventory of ribosome biogenesis factors (RBFs), they unite the highest number of orthologs to eukaryotic RBFs in one taxon. Using large ribosomal subunit maturation as an example, we demonstrate that archaea pursue a simplified version of the corresponding steps in eukaryotes. Much of the complexity of this process evolved on the eukaryotic lineage by the duplication of ribosomal proteins and their subsequent functional diversification into ribosome biogenesis factors. This highlights that studying ribosome biogenesis in archaea provides fundamental information also for understanding the process in eukaryotes.
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Affiliation(s)
- Mehmet Birikmen
- Applied Bioinformatics Group, Institute of Cell Biology and Neuroscience, Goethe University Frankfurt, Frankfurt, Germany
| | - Katherine E Bohnsack
- Department of Molecular Biology, University Medical Center Göttingen, Göttingen, Germany
| | - Vinh Tran
- Applied Bioinformatics Group, Institute of Cell Biology and Neuroscience, Goethe University Frankfurt, Frankfurt, Germany
| | - Sharvari Somayaji
- Applied Bioinformatics Group, Institute of Cell Biology and Neuroscience, Goethe University Frankfurt, Frankfurt, Germany
| | - Markus T Bohnsack
- Department of Molecular Biology, University Medical Center Göttingen, Göttingen, Germany.,Göttingen Center for Molecular Biosciences, Georg-August University, Göttingen, Germany
| | - Ingo Ebersberger
- Applied Bioinformatics Group, Institute of Cell Biology and Neuroscience, Goethe University Frankfurt, Frankfurt, Germany.,Senckenberg Biodiversity and Climate Research Center (S-BIK-F), Frankfurt, Germany.,LOEWE Center for Translational Biodiversity Genomics (LOEWE-TBG), Frankfurt, Germany
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8
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Bhaskar V, Desogus J, Graff-Meyer A, Schenk AD, Cavadini S, Chao JA. Dynamic association of human Ebp1 with the ribosome. RNA (NEW YORK, N.Y.) 2021; 27:411-419. [PMID: 33479117 PMCID: PMC7962488 DOI: 10.1261/rna.077602.120] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/12/2020] [Accepted: 01/02/2021] [Indexed: 05/09/2023]
Abstract
Ribosomes are the macromolecular machines at the heart of protein synthesis; however, their function can be modulated by a variety of additional protein factors that directly interact with them. Here, we report the cryo-EM structure of human Ebp1 (p48 isoform) bound to the human 80S ribosome at 3.3 Å resolution. Ebp1 binds in the vicinity of the peptide exit tunnel on the 80S ribosome, and this binding is enhanced upon puromycin-mediated translational inhibition. The association of Ebp1 with the 80S ribosome centers around its interaction with ribosomal proteins eL19 and uL23 and the 28S rRNA. Further analysis of the Ebp1-ribosome complex suggests that Ebp1 can rotate around its insert domain, which may enable it to assume a wide range of conformations while maintaining its interaction with the ribosome. Structurally, Ebp1 shares homology with the methionine aminopeptidase 2 family of enzymes; therefore, this inherent flexibility may also be conserved.
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Affiliation(s)
- Varun Bhaskar
- Friedrich Miescher Institute for Biomedical Research, CH-4058 Basel, Switzerland
| | - Jessica Desogus
- Friedrich Miescher Institute for Biomedical Research, CH-4058 Basel, Switzerland
- University of Basel, CH-4003 Basel, Switzerland
| | | | - Andreas D Schenk
- Friedrich Miescher Institute for Biomedical Research, CH-4058 Basel, Switzerland
| | - Simone Cavadini
- Friedrich Miescher Institute for Biomedical Research, CH-4058 Basel, Switzerland
| | - Jeffrey A Chao
- Friedrich Miescher Institute for Biomedical Research, CH-4058 Basel, Switzerland
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9
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A Small Cysteine-Free Protein Acts as a Novel Regulator of Fungal Insect-Pathogenic Lifecycle and Genomic Expression. mSystems 2021; 6:6/2/e00098-21. [PMID: 33758028 PMCID: PMC8546967 DOI: 10.1128/msystems.00098-21] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Small secreted proteins (SSPs), particularly cysteine-rich proteins secreted during fungal infection, comprise virulence effectors in plant-pathogenic fungi but remain unknown in insect-pathogenic fungi. We report here that only a small cysteine-free protein (CFP) is indispensable for insect pathogenicity of Beauveria bassiana among 10 studied SSPs (99 to 274 amino acids [aa]), including seven hypothetical proteins containing 0 to 12 Cys residues. CFP (120 aa) features an N-terminal signal peptide (residues 1 to 17), a nuclear localization signal motif (residues 24 to 57), and no predictable domain. Its homologs exist exclusively in insect-pathogenic Cordycipitaceae and Clavicipitaceae. Fluorescence-tagged CFP fusion protein was localized in the nucleus but extracellularly undetectable, suggesting an inability for CFP to be secreted out. Disruption of cfp resulted in abolished pathogenicity via normal cuticle infection, attenuated virulence via hemocoel injection, compromised conidiation capacity versus little growth defect, impaired conidial coat, blocked secretion of cuticle-degrading enzymes, impeded proliferation in vivo, disturbed cell cycle, reduced stress tolerance, and 1,818 dysregulated genes (genomic 17.54%). Hundreds of those genes correlated with phenotypic changes observed in the disruption mutant. Intriguingly, nearly 40% of those dysregulated genes encode hypothetical or unknown proteins, and another 13% encode transcription factors and enzymes or proteins collectively involved in genome-wide gene regulation. However, purified CFP showed no DNA-binding activity in an electrophoretic mobility shift assay. These findings unveil that CFP is a novel regulator of fungal insect-pathogenic life cycle and genomic expression and that cysteine richness is dispensable for distinguishing virulence effectors from putative SSPs in B. bassiana IMPORTANCE Small cysteine-rich proteins secreted during plant-pathogenic fungal infection comprise virulence effectors. Our study confirms that only a cysteine-free protein (CFP) is determinant to insect-pathogenic fungal virulence among 10 small putatively secreted proteins containing 0 to 12 Cys residues. Disruption of cfp abolished insect pathogenicity and caused not only a series of compromised cellular events associated with host infection and disease development but also dysregulation of 1,818 genes, although no DNA-binding activity was detected in purified CFP samples. Nearly 13% of those genes encode transcription factors and enzymes or proteins collectively involved in transcriptional regulation. Altogether, CFP serves as a novel regulator of the fungal insect-pathogenic life cycle and genomic expression. Cysteine richness is dispensable for distinguishing virulence effectors from the fungal SSPs.
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10
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Lacoux C, Wacheul L, Saraf K, Pythoud N, Huvelle E, Figaro S, Graille M, Carapito C, Lafontaine DLJ, Heurgué-Hamard V. The catalytic activity of the translation termination factor methyltransferase Mtq2-Trm112 complex is required for large ribosomal subunit biogenesis. Nucleic Acids Res 2020; 48:12310-12325. [PMID: 33166396 PMCID: PMC7708063 DOI: 10.1093/nar/gkaa972] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2019] [Revised: 10/05/2020] [Accepted: 10/09/2020] [Indexed: 01/14/2023] Open
Abstract
The Mtq2-Trm112 methyltransferase modifies the eukaryotic translation termination factor eRF1 on the glutamine side chain of a universally conserved GGQ motif that is essential for release of newly synthesized peptides. Although this modification is found in the three domains of life, its exact role in eukaryotes remains unknown. As the deletion of MTQ2 leads to severe growth impairment in yeast, we have investigated its role further and tested its putative involvement in ribosome biogenesis. We found that Mtq2 is associated with nuclear 60S subunit precursors, and we demonstrate that its catalytic activity is required for nucleolar release of pre-60S and for efficient production of mature 5.8S and 25S rRNAs. Thus, we identify Mtq2 as a novel ribosome assembly factor important for large ribosomal subunit formation. We propose that Mtq2-Trm112 might modify eRF1 in the nucleus as part of a quality control mechanism aimed at proof-reading the peptidyl transferase center, where it will subsequently bind during translation termination.
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Affiliation(s)
- Caroline Lacoux
- UMR8261 (CNRS, Université de Paris), Institut de Biologie Physico-Chimique, 13 rue Pierre et Marie Curie, 75005 Paris, France
| | - Ludivine Wacheul
- RNA Molecular Biology, Fonds de la Recherche Scientifique (F.R.S.-FNRS), Université Libre de Bruxelles Cancer Research Center (U-CRC), Center for Microscopy and Molecular Imaging (CMMI), Gosselies, Belgium
| | - Kritika Saraf
- RNA Molecular Biology, Fonds de la Recherche Scientifique (F.R.S.-FNRS), Université Libre de Bruxelles Cancer Research Center (U-CRC), Center for Microscopy and Molecular Imaging (CMMI), Gosselies, Belgium
| | - Nicolas Pythoud
- Laboratoire de Spectrométrie de Masse Bio-Organique (LSMBO), UMR 7178, IPHC, Université de Strasbourg, CNRS, Strasbourg, France
| | - Emmeline Huvelle
- UMR8261 (CNRS, Université de Paris), Institut de Biologie Physico-Chimique, 13 rue Pierre et Marie Curie, 75005 Paris, France
| | - Sabine Figaro
- UMR8261 (CNRS, Université de Paris), Institut de Biologie Physico-Chimique, 13 rue Pierre et Marie Curie, 75005 Paris, France
| | - Marc Graille
- Laboratoire de Biologie Structurale de la Cellule (BIOC), CNRS, Ecole polytechnique, Institut Polytechnique de Paris, F-91128 Palaiseau, France
| | - Christine Carapito
- Laboratoire de Spectrométrie de Masse Bio-Organique (LSMBO), UMR 7178, IPHC, Université de Strasbourg, CNRS, Strasbourg, France
| | - Denis L J Lafontaine
- RNA Molecular Biology, Fonds de la Recherche Scientifique (F.R.S.-FNRS), Université Libre de Bruxelles Cancer Research Center (U-CRC), Center for Microscopy and Molecular Imaging (CMMI), Gosselies, Belgium
| | - Valérie Heurgué-Hamard
- UMR8261 (CNRS, Université de Paris), Institut de Biologie Physico-Chimique, 13 rue Pierre et Marie Curie, 75005 Paris, France
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11
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Guha S, Bhaumik SR. Viral regulation of mRNA export with potentials for targeted therapy. BIOCHIMICA ET BIOPHYSICA ACTA-GENE REGULATORY MECHANISMS 2020; 1864:194655. [PMID: 33246183 DOI: 10.1016/j.bbagrm.2020.194655] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Subscribe] [Scholar Register] [Received: 07/04/2020] [Revised: 10/15/2020] [Accepted: 11/05/2020] [Indexed: 12/12/2022]
Abstract
Eukaryotic gene expression begins with transcription in the nucleus to synthesize mRNA (messenger RNA), which is subsequently exported to the cytoplasm for translation to protein. Like transcription and translation, mRNA export is an important regulatory step of eukaryotic gene expression. Various factors are involved in regulating mRNA export, and thus gene expression. Intriguingly, some of these factors interact with viral proteins, and such interactions interfere with mRNA export of the host cell, favoring viral RNA export. Hence, viruses hijack host mRNA export machinery for export of their own RNAs from nucleus to cytoplasm for translation to proteins for viral life cycle, suppressing host mRNA export (and thus host gene expression and immune/antiviral response). Therefore, the molecules that can impair the interactions of these mRNA export factors with viral proteins could emerge as antiviral therapeutic agents to suppress viral RNA transport and enhance host mRNA export, thereby promoting host gene expression and immune response. Thus, there has been a number of studies to understand how virus hijacks mRNA export machinery in suppressing host gene expression and promoting its own RNA export to the cytoplasm for translation to proteins required for viral replication/assembly/life cycle towards developing targeted antiviral therapies, as concisely described here.
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Affiliation(s)
- Shalini Guha
- Department of Biochemistry and Molecular Biology, Southern Illinois University School of Medicine, Carbondale, IL 62901, USA
| | - Sukesh R Bhaumik
- Department of Biochemistry and Molecular Biology, Southern Illinois University School of Medicine, Carbondale, IL 62901, USA.
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12
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Musalgaonkar S, Black JJ, Johnson AW. The L1 stalk is required for efficient export of nascent large ribosomal subunits in yeast. RNA (NEW YORK, N.Y.) 2019; 25:1549-1560. [PMID: 31439809 PMCID: PMC6795138 DOI: 10.1261/rna.071811.119] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/08/2019] [Accepted: 08/08/2019] [Indexed: 06/02/2023]
Abstract
The ribosomal protein Rpl1 (uL1 in universal nomenclature) is essential in yeast and constitutes part of the L1 stalk which interacts with E site ligands on the ribosome. Structural studies of nascent pre-60S complexes in yeast have shown that a domain of the Crm1-dependent nuclear export adapter Nmd3, binds in the E site and interacts with Rpl1, inducing closure of the L1 stalk. Based on this observation, we decided to reinvestigate the role of the L1 stalk in nuclear export of pre-60S subunits despite previous work showing that Rpl1-deficient ribosomes are exported from the nucleus and engage in translation. Large cargoes, such as ribosomal subunits, require multiple export factors to facilitate their transport through the nuclear pore complex. Here, we show that pre-60S subunits lacking Rpl1 or truncated for the RNA of the L1 stalk are exported inefficiently. Surprisingly, this is not due to a measurable defect in the recruitment of Nmd3 but appears to result from inefficient recruitment of the Mex67-Mtr2 heterodimer.
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Affiliation(s)
- Sharmishtha Musalgaonkar
- Department of Molecular Biosciences, The University of Texas at Austin, Austin, Texas 78712, USA
| | - Joshua J Black
- Department of Molecular Biosciences, The University of Texas at Austin, Austin, Texas 78712, USA
| | - Arlen W Johnson
- Department of Molecular Biosciences, The University of Texas at Austin, Austin, Texas 78712, USA
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13
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Lari A, Arul Nambi Rajan A, Sandhu R, Reiter T, Montpetit R, Young BP, Loewen CJ, Montpetit B. A nuclear role for the DEAD-box protein Dbp5 in tRNA export. eLife 2019; 8:48410. [PMID: 31453808 PMCID: PMC6711706 DOI: 10.7554/elife.48410] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/13/2019] [Accepted: 08/09/2019] [Indexed: 01/01/2023] Open
Abstract
Dbp5 is an essential DEAD-box protein that mediates nuclear mRNP export. Dbp5 also shuttles between nuclear and cytoplasmic compartments with reported roles in transcription, ribosomal subunit export, and translation; however, the mechanism(s) by which nucleocytoplasmic transport occurs and how Dbp5 specifically contributes to each of these processes remains unclear. Towards understanding the functions and transport of Dbp5 in Saccharomyces cerevisiae, alanine scanning mutagenesis was used to generate point mutants at all possible residues within a GFP-Dbp5 reporter. Characterization of the 456 viable mutants led to the identification of an N-terminal Xpo1-dependent nuclear export signal in Dbp5, in addition to other separation-of-function alleles, which together provide evidence that Dbp5 nuclear shuttling is not essential for mRNP export. Rather, disruptions in Dbp5 nucleocytoplasmic transport result in tRNA export defects, including changes in tRNA shuttling dynamics during recovery from nutrient stress.
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Affiliation(s)
- Azra Lari
- Department of Cell Biology, University of Alberta, Edmonton, Canada
| | - Arvind Arul Nambi Rajan
- Biochemistry, Molecular, Cellular and Developmental Biology Graduate Group, University of California, Davis, Davis, United States
| | - Rima Sandhu
- Department of Viticulture and Enology, University of California, Davis, Davis, United States
| | - Taylor Reiter
- Food Science Graduate Group, University of California Davis, Davis, United States
| | - Rachel Montpetit
- Department of Viticulture and Enology, University of California, Davis, Davis, United States
| | - Barry P Young
- Department of Cellular and Physiological Sciences, Life Sciences Institute, University of British Columbia, Vancouver, Canada
| | - Chris Jr Loewen
- Department of Cellular and Physiological Sciences, Life Sciences Institute, University of British Columbia, Vancouver, Canada
| | - Ben Montpetit
- Department of Cell Biology, University of Alberta, Edmonton, Canada.,Biochemistry, Molecular, Cellular and Developmental Biology Graduate Group, University of California, Davis, Davis, United States.,Department of Viticulture and Enology, University of California, Davis, Davis, United States.,Food Science Graduate Group, University of California Davis, Davis, United States
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14
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Shao W, Cai Q, Tong SM, Ying SH, Feng MG. Rei1-like protein regulates nutritional metabolism and transport required for the asexual cycle in vitro and in vivo of a fungal insect pathogen. Environ Microbiol 2019; 21:2772-2786. [PMID: 30932324 DOI: 10.1111/1462-2920.14616] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/20/2018] [Accepted: 03/31/2019] [Indexed: 12/12/2022]
Abstract
Rei1 is a cytoplasm-specific pre-60S subunit export factor that functions exclusively in cold-sensitive yeast growth but remains unexplored in filamentous fungi. Here, we report that Rei1-like BbRei1 is localized in both cytoplasm and nucleus and acts as a vital regulator in Beauveria bassiana. Deletion of BbRei1 resulted in delayed conidial germination, abnormally polarized germlings, severe growth defects on various carbon/nitrogen sources and reduced conidiation capacity as well as low temperature-sensitive growth. In ΔBbrei1, greatly attenuated virulence correlated with reduced activities of enzymes secreted for cuticular penetration and blocked formation of hyphal bodies in vivo essential for facilitation of host mummification. Revealed by transcriptomic analysis, 560 and 840 genes were significantly up- and down-regulated in ΔBbrei1 versus wild-type respectively, representing 13.5% of the fungal genome. Many repressed genes were involved in metabolism and transport of carbohydrates and amino acids. However, electrophoretic mobility shift assays presented no interactions of purified BbRei1 with 14 promoter DNA fragments. Conclusively, BbRei1 plays a pivotal role in gene expression and metabolism of nutrients and energy essential for the asexual cycle in vitro and in vivo of B. bassiana and functions much beyond the role for the yeast Rei1 in cold-sensitive cell growth.
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Affiliation(s)
- Wei Shao
- MOE Laboratory of Biosystems Homeostasis & Protection, Institute of Microbiology, College of Life Sciences, Zhejiang University, Hangzhou, Zhejiang 310058, China
| | - Qing Cai
- MOE Laboratory of Biosystems Homeostasis & Protection, Institute of Microbiology, College of Life Sciences, Zhejiang University, Hangzhou, Zhejiang 310058, China
| | - Sen-Miao Tong
- MOE Laboratory of Biosystems Homeostasis & Protection, Institute of Microbiology, College of Life Sciences, Zhejiang University, Hangzhou, Zhejiang 310058, China.,College of Agricultural and Food Science, Zhejiang A&F University, Lin'an, Zhejiang 311300, China
| | - Sheng-Hua Ying
- MOE Laboratory of Biosystems Homeostasis & Protection, Institute of Microbiology, College of Life Sciences, Zhejiang University, Hangzhou, Zhejiang 310058, China
| | - Ming-Guang Feng
- MOE Laboratory of Biosystems Homeostasis & Protection, Institute of Microbiology, College of Life Sciences, Zhejiang University, Hangzhou, Zhejiang 310058, China
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15
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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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16
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Bosio MC, Fermi B, Spagnoli G, Levati E, Rubbi L, Ferrari R, Pellegrini M, Dieci G. Abf1 and other general regulatory factors control ribosome biogenesis gene expression in budding yeast. Nucleic Acids Res 2017; 45:4493-4506. [PMID: 28158860 PMCID: PMC5416754 DOI: 10.1093/nar/gkx058] [Citation(s) in RCA: 26] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/14/2016] [Accepted: 01/25/2017] [Indexed: 01/21/2023] Open
Abstract
Ribosome biogenesis in Saccharomyces cerevisiae involves a regulon of >200 genes (Ribi genes) coordinately regulated in response to nutrient availability and cellular growth rate. Two cis-acting elements called PAC and RRPE are known to mediate Ribi gene repression in response to nutritional downshift. Here, we show that most Ribi gene promoters also contain binding sites for one or more General Regulatory Factors (GRFs), most frequently Abf1 and Reb1, and that these factors are enriched in vivo at Ribi promoters. Abf1/Reb1/Tbf1 promoter association was required for full Ribi gene expression in rich medium and for its modulation in response to glucose starvation, characterized by a rapid drop followed by slow recovery. Such a response did not entail changes in Abf1 occupancy, but it was paralleled by a quick increase, followed by slow decrease, in Rpd3L histone deacetylase occupancy. Remarkably, Abf1 site disruption also abolished Rpd3L complex recruitment in response to starvation. Extensive mutational analysis of the DBP7 promoter revealed a complex interplay of Tbf1 sites, PAC and RRPE in the transcriptional regulation of this Ribi gene. Our observations point to GRFs as new multifaceted players in Ribi gene regulation both during exponential growth and under repressive conditions.
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Affiliation(s)
- Maria Cristina Bosio
- Department of Chemistry, Life Sciences and Environmental Sustainability, University of Parma, Parco Area delle Scienze 23/A, 43124 Parma, Italy
| | - Beatrice Fermi
- Department of Chemistry, Life Sciences and Environmental Sustainability, University of Parma, Parco Area delle Scienze 23/A, 43124 Parma, Italy
| | - Gloria Spagnoli
- Department of Chemistry, Life Sciences and Environmental Sustainability, University of Parma, Parco Area delle Scienze 23/A, 43124 Parma, Italy
| | - Elisabetta Levati
- Department of Chemistry, Life Sciences and Environmental Sustainability, University of Parma, Parco Area delle Scienze 23/A, 43124 Parma, Italy
| | - Ludmilla Rubbi
- Department of Molecular, Cell and Developmental Biology, University of California Los Angeles, Los Angeles, CA 90095, USA
| | - Roberto Ferrari
- Department of Molecular, Cell and Developmental Biology, University of California Los Angeles, Los Angeles, CA 90095, USA
| | - Matteo Pellegrini
- Department of Molecular, Cell and Developmental Biology, University of California Los Angeles, Los Angeles, CA 90095, USA
| | - Giorgio Dieci
- Department of Chemistry, Life Sciences and Environmental Sustainability, University of Parma, Parco Area delle Scienze 23/A, 43124 Parma, Italy
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17
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Rogell B, Fischer B, Rettel M, Krijgsveld J, Castello A, Hentze MW. Specific RNP capture with antisense LNA/DNA mixmers. RNA (NEW YORK, N.Y.) 2017; 23:1290-1302. [PMID: 28476952 PMCID: PMC5513073 DOI: 10.1261/rna.060798.117] [Citation(s) in RCA: 29] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/17/2017] [Accepted: 04/25/2017] [Indexed: 05/07/2023]
Abstract
RNA-binding proteins (RBPs) play essential roles in RNA biology, responding to cellular and environmental stimuli to regulate gene expression. Important advances have helped to determine the (near) complete repertoires of cellular RBPs. However, identification of RBPs associated with specific transcripts remains a challenge. Here, we describe "specific ribonucleoprotein (RNP) capture," a versatile method for the determination of the proteins bound to specific transcripts in vitro and in cellular systems. Specific RNP capture uses UV irradiation to covalently stabilize protein-RNA interactions taking place at "zero distance." Proteins bound to the target RNA are captured by hybridization with antisense locked nucleic acid (LNA)/DNA oligonucleotides covalently coupled to a magnetic resin. After stringent washing, interacting proteins are identified by quantitative mass spectrometry. Applied to in vitro extracts, specific RNP capture identifies the RBPs bound to a reporter mRNA containing the Sex-lethal (Sxl) binding motifs, revealing that the Sxl homolog sister of Sex lethal (Ssx) displays similar binding preferences. This method also revealed the repertoire of RBPs binding to 18S or 28S rRNAs in HeLa cells, including previously unknown rRNA-binding proteins.
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Affiliation(s)
- Birgit Rogell
- European Molecular Biology Laboratory (EMBL), 69117 Heidelberg, Germany
| | - Bernd Fischer
- European Molecular Biology Laboratory (EMBL), 69117 Heidelberg, Germany
- German Cancer Research Center (DKFZ), 69120 Heidelberg, Germany
| | - Mandy Rettel
- European Molecular Biology Laboratory (EMBL), 69117 Heidelberg, Germany
| | - Jeroen Krijgsveld
- European Molecular Biology Laboratory (EMBL), 69117 Heidelberg, Germany
- German Cancer Research Center (DKFZ), 69120 Heidelberg, Germany
| | - Alfredo Castello
- European Molecular Biology Laboratory (EMBL), 69117 Heidelberg, Germany
- Department of Biochemistry, University of Oxford, Oxford, OX1 3QU, United Kingdom
| | - Matthias W Hentze
- European Molecular Biology Laboratory (EMBL), 69117 Heidelberg, Germany
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18
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Patchett S, Musalgaonkar S, Malyutin AG, Johnson AW. The T-cell leukemia related rpl10-R98S mutant traps the 60S export adapter Nmd3 in the ribosomal P site in yeast. PLoS Genet 2017; 13:e1006894. [PMID: 28715419 PMCID: PMC5536393 DOI: 10.1371/journal.pgen.1006894] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/01/2017] [Revised: 07/31/2017] [Accepted: 06/23/2017] [Indexed: 12/12/2022] Open
Abstract
Mutations in the ribosomal protein Rpl10 (uL16) can be drivers of T-cell acute lymphoblastic leukemia (T-ALL). We previously showed that these T-ALL mutations disrupt late cytoplasmic maturation of the 60S ribosomal subunit, blocking the release of the trans-acting factors Nmd3 and Tif6 in S. cerevisiae. Consequently, these mutant ribosomes do not efficiently pass the cytoplasmic quality control checkpoint and are blocked from engaging in translation. Here, we characterize suppressing mutations of the T-ALL-related rpl10-R98S mutant that bypass this block and show that the molecular defect of rpl10-R98S is a failure to release Nmd3 from the P site. Suppressing mutations were identified in Nmd3 and Tif6 that disrupted interactions between Nmd3 and the ribosome, or between Nmd3 and Tif6. Using an in vitro system with purified components, we found that Nmd3 inhibited Sdo1-stimulated Efl1 activity on mutant rpl10-R98S but not wild-type 60S subunits. Importantly, this inhibition was overcome in vitro by mutations in Nmd3 that suppressed rpl10-R98S in vivo. These results strongly support a model that Nmd3 must be dislodged from the P site to allow Sdo1 activation of Efl1, and define a failure in the removal of Nmd3 as the molecular defect of the T-ALL-associated rpl10-R98S mutation. The ribosome is a large and structurally complex macromolecular machine, responsible for synthesizing proteins in all living cells, across all domains of life. The correct assembly of ribosomes is important for their ability to faithfully decode messenger RNAs and synthesize proteins. The insertion of the ribosomal protein Rpl10 into the ribosome completes the catalytic center of the large subunit and is necessary for the removal of the assembly factors Nmd3 and Tif6, which allows the subunit to participate in translation. The insertion of Rpl10 is monitored by proteins that mimic translation factors during a quality control check for ribosome function. Ribosomes containing mutations in Rpl10 associated with pediatric T-cell leukemia fail in this quality control check and prevent the removal of Tif6 and Nmd3. However, it was not known how these mutations in Rpl10 block the quality control check. We recently presented the structure of Nmd3 and Tif6 on the large ribosomal subunit from yeast. In this work, we take advantage of our recent structural work and use a combination of genetic and biochemical techniques to delineate the molecular defect in the ribosome when Rpl10 is mutated.
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Affiliation(s)
- Stephanie Patchett
- Depatment of Molecular Biosciences, the University of Texas at Austin, Austin, Texas, United States of America
| | - Sharmishtha Musalgaonkar
- Depatment of Molecular Biosciences, the University of Texas at Austin, Austin, Texas, United States of America
| | - Andrey G Malyutin
- Department of Biochemistry and Molecular Biophysics, Columbia University, New York, New York, United States of America
| | - Arlen W Johnson
- Depatment of Molecular Biosciences, the University of Texas at Austin, Austin, Texas, United States of America
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19
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Dai Y, Kennedy-Darling J, Shortreed MR, Scalf M, Gasch AP, Smith LM. Multiplexed Sequence-Specific Capture of Chromatin and Mass Spectrometric Discovery of Associated Proteins. Anal Chem 2017; 89:7841-7846. [PMID: 28654248 DOI: 10.1021/acs.analchem.7b01784] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
Comprehensive understanding of a gene's expression and regulation at the molecular level requires identification of all proteins interacting with the gene. HyCCAPP (Hybridization Capture of Chromatin Associated Proteins for Proteomics) is an approach that uses single-stranded DNA oligonucleotides to capture specific genomic sequences in cross-linked chromatin fragments and identify associated proteins by mass spectrometry. Previous studies have shown HyCCAPP to provide useful information on protein-DNA interactions, revealing the proteins associated with the GAL1-10 region in yeast. We present here a multiplexed version of HyCCAPP. Utilizing a toehold-mediated capture/release strategy, HyCCAPP is targeted to multiple genomic loci in parallel, and the protein binders at each locus are eluted in a programmable and selective fashion. Multiplexed HyCCAPP was applied to four genes (25S rDNA, ARX1, CTT1, and RPL30) in S. cerevisiae under normal and stressed conditions. Capture and release efficiencies and specificities were comparable to those obtained without multiplexing. Using mass spectrometry-based bottom-up proteomics, hundreds of proteins were discovered at each locus in each condition. Statistical analysis revealed 34-88 enriched proteins in each gene capture. Many of these proteins had expected functions, including DNA-related and ribosome biogenesis-associated activities. Multiplexed HyCCAPP provides a useful strategy for the identification of proteins interacting with specific chromatin regions.
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Affiliation(s)
- Yunxiang Dai
- Department of Chemistry, University of Wisconsin , 1101 University Avenue, Madison, Wisconsin 53706, United States
| | - Julia Kennedy-Darling
- Department of Chemistry, University of Wisconsin , 1101 University Avenue, Madison, Wisconsin 53706, United States
| | - Michael R Shortreed
- Department of Chemistry, University of Wisconsin , 1101 University Avenue, Madison, Wisconsin 53706, United States
| | - Mark Scalf
- Department of Chemistry, University of Wisconsin , 1101 University Avenue, Madison, Wisconsin 53706, United States
| | - Audrey P Gasch
- Laboratory of Genetics, University of Wisconsin , 425 Henry Mall, Madison, Wisconsin 53706, United States
| | - Lloyd M Smith
- Department of Chemistry, University of Wisconsin , 1101 University Avenue, Madison, Wisconsin 53706, United States.,Genome Center of Wisconsin, University of Wisconsin , 425G Henry Mall, Room 3420, Madison, Wisconsin 53706, United States
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20
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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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21
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Malyutin AG, Musalgaonkar S, Patchett S, Frank J, Johnson AW. Nmd3 is a structural mimic of eIF5A, and activates the cpGTPase Lsg1 during 60S ribosome biogenesis. EMBO J 2017; 36:854-868. [PMID: 28179369 PMCID: PMC5376978 DOI: 10.15252/embj.201696012] [Citation(s) in RCA: 53] [Impact Index Per Article: 7.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/03/2016] [Revised: 01/17/2017] [Accepted: 01/18/2017] [Indexed: 12/22/2022] Open
Abstract
During ribosome biogenesis in eukaryotes, nascent subunits are exported to the cytoplasm in a functionally inactive state. 60S subunits are activated through a series of cytoplasmic maturation events. The last known events in the cytoplasm are the release of Tif6 by Efl1 and Sdo1 and the release of the export adapter, Nmd3, by the GTPase Lsg1. Here, we have used cryo-electron microscopy to determine the structure of the 60S subunit bound by Nmd3, Lsg1, and Tif6. We find that a central domain of Nmd3 mimics the translation elongation factor eIF5A, inserting into the E site of the ribosome and pulling the L1 stalk into a closed position. Additional domains occupy the P site and extend toward the sarcin-ricin loop to interact with Tif6. Nmd3 and Lsg1 together embrace helix 69 of the B2a intersubunit bridge, inducing base flipping that we suggest may activate the GTPase activity of Lsg1.
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Affiliation(s)
- Andrey G Malyutin
- Department of Biochemistry and Molecular Biophysics, Columbia University, New York, NY, USA
| | | | - Stephanie Patchett
- Department of Molecular Biosciences, The University of Texas at Austin, Austin, TX, USA
| | - Joachim Frank
- Department of Biochemistry and Molecular Biophysics, Columbia University, New York, NY, USA
- Department of Biological Sciences, Columbia University, New York, NY, USA
- Howard Hughes Medical Institute, Columbia University, New York, NY, USA
| | - Arlen W Johnson
- Department of Molecular Biosciences, The University of Texas at Austin, Austin, TX, USA
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22
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Structural snapshot of cytoplasmic pre-60S ribosomal particles bound by Nmd3, Lsg1, Tif6 and Reh1. Nat Struct Mol Biol 2017; 24:214-220. [PMID: 28112732 DOI: 10.1038/nsmb.3364] [Citation(s) in RCA: 70] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/22/2016] [Accepted: 12/19/2016] [Indexed: 01/01/2023]
Abstract
A key step in ribosome biogenesis is the nuclear export of pre-ribosomal particles. Nmd3, a highly conserved protein in eukaryotes, is a specific adaptor required for the export of pre-60S particles. Here we used cryo-electron microscopy (cryo-EM) to characterize Saccharomyces cerevisiae pre-60S particles purified with epitope-tagged Nmd3. Our structural analysis indicates that these particles belong to a specific late stage of cytoplasmic pre-60S maturation in which ribosomal proteins uL16, uL10, uL11, eL40 and eL41 are deficient, but ribosome assembly factors Nmd3, Lsg1, Tif6 and Reh1 are present. Nmd3 and Lsg1 are located near the peptidyl-transferase center (PTC). In particular, Nmd3 recognizes the PTC in its near-mature conformation. In contrast, Reh1 is anchored to the exit of the polypeptide tunnel, with its C terminus inserted into the tunnel. These findings pinpoint a structural checkpoint role for Nmd3 in PTC assembly, and provide information about functional and mechanistic roles of these assembly factors in the maturation of the 60S ribosomal subunit.
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23
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Bredeweg EL, Pomraning KR, Dai Z, Nielsen J, Kerkhoven EJ, Baker SE. A molecular genetic toolbox for Yarrowia lipolytica. BIOTECHNOLOGY FOR BIOFUELS 2017; 10:2. [PMID: 28066508 PMCID: PMC5210315 DOI: 10.1186/s13068-016-0687-7] [Citation(s) in RCA: 37] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/24/2016] [Accepted: 12/13/2016] [Indexed: 05/29/2023]
Abstract
BACKGROUND Yarrowia lipolytica is an ascomycete yeast used in biotechnological research for its abilities to secrete high concentrations of proteins and accumulate lipids. Genetic tools have been made in a variety of backgrounds with varying similarity to a comprehensively sequenced strain. RESULTS We have developed a set of genetic and molecular tools in order to expand capabilities of Y. lipolytica for both biological research and industrial bioengineering applications. In this work, we generated a set of isogenic auxotrophic strains with decreased non-homologous end joining for targeted DNA incorporation. Genome sequencing, assembly, and annotation of this genetic background uncovers previously unidentified genes in Y. lipolytica. To complement these strains, we constructed plasmids with Y. lipolytica-optimized superfolder GFP for targeted overexpression and fluorescent tagging. We used these tools to build the "Yarrowia lipolytica Cell Atlas," a collection of strains with endogenous fluorescently tagged organelles in the same genetic background, in order to define organelle morphology in live cells. CONCLUSIONS These molecular and isogenetic tools are useful for live assessment of organelle-specific protein expression, and for localization of lipid biosynthetic enzymes or other proteins in Y. lipolytica. This work provides the Yarrowia community with tools for cell biology and metabolism research in Y. lipolytica for further development of biofuels and natural products.
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Affiliation(s)
- Erin L. Bredeweg
- Earth and Biological Sciences Directorate, Environmental Molecular Sciences Laboratory, Richland, WA 99354 USA
- Department of Energy, Battelle EMSL, 3335 Innovation Blvd, Richland, WA 99354 USA
| | - Kyle R. Pomraning
- Chemical & Biological Process Development Group, Energy and Environment Directorate, Pacific Northwest National Laboratories, Richland, WA 99354 USA
| | - Ziyu Dai
- Chemical & Biological Process Development Group, Energy and Environment Directorate, Pacific Northwest National Laboratories, Richland, WA 99354 USA
| | - Jens Nielsen
- Systems and Synthetic Biology, Department of Biology and Biological Engineering, Chalmers University of Technology, Göteborg, Sweden
- Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, Hørsholm, Denmark
| | - Eduard J. Kerkhoven
- Systems and Synthetic Biology, Department of Biology and Biological Engineering, Chalmers University of Technology, Göteborg, Sweden
| | - Scott E. Baker
- Earth and Biological Sciences Directorate, Environmental Molecular Sciences Laboratory, Richland, WA 99354 USA
- Department of Energy, Battelle EMSL, 3335 Innovation Blvd, Richland, WA 99354 USA
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24
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Ting YH, Lu TJ, Johnson AW, Shie JT, Chen BR, Kumar S S, Lo KY. Bcp1 Is the Nuclear Chaperone of Rpl23 in Saccharomyces cerevisiae. J Biol Chem 2016; 292:585-596. [PMID: 27913624 DOI: 10.1074/jbc.m116.747634] [Citation(s) in RCA: 29] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/09/2016] [Revised: 11/21/2016] [Indexed: 12/18/2022] Open
Abstract
Eukaryotic ribosomes are composed of rRNAs and ribosomal proteins. Ribosomal proteins are translated in the cytoplasm and imported into the nucleus for assembly with the rRNAs. It has been shown that chaperones or karyopherins responsible for import can maintain the stability of ribosomal proteins by neutralizing unfavorable positive charges and thus facilitate their transports. Among 79 ribosomal proteins in yeast, only a few are identified with specific chaperones. Besides the classic role in maintaining protein stability, chaperones have additional roles in transport, chaperoning the assembly site, and dissociation of ribosomal proteins from karyopherins. Bcp1 has been shown to be necessary for the export of Mss4, a phosphatidylinositol 4-phosphate 5-kinase, and required for ribosome biogenesis. However, its specific function in ribosome biogenesis has not been described. Here, we show that Bcp1 dissociates Rpl23 from the karyopherins and associates with Rpl23 afterward. Loss of Bcp1 causes instability of Rpl23 and deficiency of 60S subunits. In summary, Bcp1 is a novel 60S biogenesis factor via chaperoning Rpl23 in the nucleus.
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Affiliation(s)
- Ya-Han Ting
- From the Department of Agricultural Chemistry, National Taiwan University, 1 Sec. 4, Roosevelt Road, Taipei 10617, Taiwan
| | - Ting-Jun Lu
- From the Department of Agricultural Chemistry, National Taiwan University, 1 Sec. 4, Roosevelt Road, Taipei 10617, Taiwan
| | - Arlen W Johnson
- the Department of Molecular Biosciences, Institute for Cellular and Molecular Biology, University of Texas, Austin, Texas 78712, and
| | - Jing-Ting Shie
- From the Department of Agricultural Chemistry, National Taiwan University, 1 Sec. 4, Roosevelt Road, Taipei 10617, Taiwan
| | - Bo-Ru Chen
- From the Department of Agricultural Chemistry, National Taiwan University, 1 Sec. 4, Roosevelt Road, Taipei 10617, Taiwan
| | - Suresh Kumar S
- From the Department of Agricultural Chemistry, National Taiwan University, 1 Sec. 4, Roosevelt Road, Taipei 10617, Taiwan.,the Department of Medical Microbiology and Parasitology, Universiti Putra Malaysia, 43400 Selangor, Malaysia
| | - Kai-Yin Lo
- From the Department of Agricultural Chemistry, National Taiwan University, 1 Sec. 4, Roosevelt Road, Taipei 10617, Taiwan,
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25
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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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26
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Sarkar A, Pech M, Thoms M, Beckmann R, Hurt E. Ribosome-stalk biogenesis is coupled with recruitment of nuclear-export factor to the nascent 60S subunit. Nat Struct Mol Biol 2016; 23:1074-1082. [PMID: 27775710 DOI: 10.1038/nsmb.3312] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/29/2016] [Accepted: 09/26/2016] [Indexed: 12/16/2022]
Abstract
Nuclear export of preribosomal subunits is a key step during eukaryotic ribosome formation. To efficiently pass through the FG-repeat meshwork of the nuclear pore complex, the large pre-60S subunit requires several export factors. Here we describe the mechanism of recruitment of the Saccharomyces cerevisiae RNA-export receptor Mex67-Mtr2 to the pre-60S subunit at the proper time. Mex67-Mtr2 binds at the premature ribosomal-stalk region, which later during translation serves as a binding platform for translational GTPases on the mature ribosome. The assembly factor Mrt4, a structural homolog of cytoplasmic-stalk protein P0, masks this site, thus preventing untimely recruitment of Mex67-Mtr2 to nuclear pre-60S particles. Subsequently, Yvh1 triggers Mrt4 release in the nucleus, thereby creating a narrow time window for Mex67-Mtr2 association at this site and facilitating nuclear export of the large subunit. Thus, a spatiotemporal mark on the ribosomal stalk controls the recruitment of an RNA-export receptor to the nascent 60S subunit.
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Affiliation(s)
- Anshuk Sarkar
- Biochemistry Centre, University of Heidelberg, Heidelberg, Germany
| | - Markus Pech
- Gene Center, University of Munich, Munich, Germany
| | - Matthias Thoms
- Biochemistry Centre, University of Heidelberg, Heidelberg, Germany
| | | | - Ed Hurt
- Biochemistry Centre, University of Heidelberg, Heidelberg, Germany
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27
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Greber BJ, Gerhardy S, Leitner A, Leibundgut M, Salem M, Boehringer D, Leulliot N, Aebersold R, Panse VG, Ban N. Insertion of the Biogenesis Factor Rei1 Probes the Ribosomal Tunnel during 60S Maturation. Cell 2015; 164:91-102. [PMID: 26709046 DOI: 10.1016/j.cell.2015.11.027] [Citation(s) in RCA: 75] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/24/2015] [Revised: 10/08/2015] [Accepted: 11/05/2015] [Indexed: 10/22/2022]
Abstract
Eukaryotic ribosome biogenesis depends on several hundred assembly factors to produce functional 40S and 60S ribosomal subunits. The final phase of 60S subunit biogenesis is cytoplasmic maturation, which includes the proofreading of functional centers of the 60S subunit and the release of several ribosome biogenesis factors. We report the cryo-electron microscopy (cryo-EM) structure of the yeast 60S subunit in complex with the biogenesis factors Rei1, Arx1, and Alb1 at 3.4 Å resolution. In addition to the network of interactions formed by Alb1, the structure reveals a mechanism for ensuring the integrity of the ribosomal polypeptide exit tunnel. Arx1 probes the entire set of inner-ring proteins surrounding the tunnel exit, and the C terminus of Rei1 is deeply inserted into the ribosomal tunnel, where it forms specific contacts along almost its entire length. We provide genetic and biochemical evidence that failure to insert the C terminus of Rei1 precludes subsequent steps of 60S maturation.
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Affiliation(s)
- Basil Johannes Greber
- Institute of Molecular Biology and Biophysics, Department of Biology, ETH Zurich, CH-8093 Zurich, Switzerland
| | - Stefan Gerhardy
- Institute of Biochemistry, Department of Biology, ETH Zurich, CH-8093 Zurich, Switzerland
| | - Alexander Leitner
- Institute of Molecular Systems Biology, Department of Biology, ETH Zurich, CH-8093 Zurich, Switzerland
| | - Marc Leibundgut
- Institute of Molecular Biology and Biophysics, Department of Biology, ETH Zurich, CH-8093 Zurich, Switzerland
| | - Michèle Salem
- Laboratoire de Cristallographie et RMN Biologiques, UMR CNRS 8015, Université Paris Descartes, Sorbonne Paris Cité, Faculté de Pharmacie, 75006 Paris, France
| | - Daniel Boehringer
- Institute of Molecular Biology and Biophysics, Department of Biology, ETH Zurich, CH-8093 Zurich, Switzerland
| | - Nicolas Leulliot
- Laboratoire de Cristallographie et RMN Biologiques, UMR CNRS 8015, Université Paris Descartes, Sorbonne Paris Cité, Faculté de Pharmacie, 75006 Paris, France
| | - Ruedi Aebersold
- Institute of Molecular Systems Biology, Department of Biology, ETH Zurich, CH-8093 Zurich, Switzerland; Faculty of Science, University of Zurich, CH-8057 Zurich, Switzerland
| | - Vikram Govind Panse
- Institute of Biochemistry, Department of Biology, ETH Zurich, CH-8093 Zurich, Switzerland.
| | - Nenad Ban
- Institute of Molecular Biology and Biophysics, Department of Biology, ETH Zurich, CH-8093 Zurich, Switzerland.
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28
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Lord CL, Timney BL, Rout MP, Wente SR. Altering nuclear pore complex function impacts longevity and mitochondrial function in S. cerevisiae. ACTA ACUST UNITED AC 2015; 208:729-44. [PMID: 25778920 PMCID: PMC4362458 DOI: 10.1083/jcb.201412024] [Citation(s) in RCA: 49] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
Specific nucleoporins and nuclear pore complex–dependent transport events directly influence aging in yeast. The eukaryotic nuclear permeability barrier and selective nucleocytoplasmic transport are maintained by nuclear pore complexes (NPCs), large structures composed of ∼30 proteins (nucleoporins [Nups]). NPC structure and function are disrupted in aged nondividing metazoan cells, although it is unclear whether these changes are a cause or consequence of aging. Using the replicative life span (RLS) of Saccharomyces cerevisiae as a model, we find that specific Nups and transport events regulate longevity independent of changes in NPC permeability. Mutants lacking the GLFG domain of Nup116 displayed decreased RLSs, whereas longevity was increased in nup100-null mutants. We show that Nup116 mediates nuclear import of the karyopherin Kap121, and each protein is required for mitochondrial function. Both Kap121-dependent transport and Nup116 levels decrease in replicatively aged yeast. Overexpression of GSP1, the small GTPase that powers karyopherin-mediated transport, rescued mitochondrial and RLS defects in nup116 mutants and increased longevity in wild-type cells. Together, these studies reveal that specific NPC nuclear transport events directly influence aging.
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Affiliation(s)
- Christopher L Lord
- Department of Cell and Developmental Biology, Vanderbilt University School of Medicine, Nashville, TN 37232
| | - Benjamin L Timney
- Laboratory of Cellular and Structural Biology, The Rockefeller University, New York, NY 10021
| | - Michael P Rout
- Laboratory of Cellular and Structural Biology, The Rockefeller University, New York, NY 10021
| | - Susan R Wente
- Department of Cell and Developmental Biology, Vanderbilt University School of Medicine, Nashville, TN 37232
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29
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Nerurkar P, Altvater M, Gerhardy S, Schütz S, Fischer U, Weirich C, Panse VG. Eukaryotic Ribosome Assembly and Nuclear Export. INTERNATIONAL REVIEW OF CELL AND MOLECULAR BIOLOGY 2015; 319:107-40. [DOI: 10.1016/bs.ircmb.2015.07.002] [Citation(s) in RCA: 78] [Impact Index Per Article: 8.7] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
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30
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Merwin JR, Bogar LB, Poggi SB, Fitch RM, Johnson AW, Lycan DE. Genetic analysis of the ribosome biogenesis factor Ltv1 of Saccharomyces cerevisiae. Genetics 2014; 198:1071-85. [PMID: 25213169 PMCID: PMC4224153 DOI: 10.1534/genetics.114.168294] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2014] [Accepted: 09/04/2014] [Indexed: 01/24/2023] Open
Abstract
Ribosome biogenesis has been studied extensively in the yeast Saccharomyces cerevisiae. Yeast Ltv1 is a conserved 40S-associated biogenesis factor that has been proposed to function in small subunit nuclear export. Here we show that Ltv1 has a canonical leucine-rich nuclear export signal (NES) at its extreme C terminus that is both necessary for Crm1 interaction and Ltv1 export. The C terminus of Ltv1 can substitute for the NES in the 60S-export adapter Nmd3, demonstrating that it is a functional NES. Overexpression of an Ltv1 lacking its NES (Ltv1∆C13) was strongly dominant negative and resulted in the nuclear accumulation of RpS3-GFP; however, export of the pre-40S was not affected. In addition, expression of endogenous levels of Ltv1∆C protein complemented both the slow-growth phenotype and the 40S biogenesis defect of an ltv1 deletion mutant. Thus, if Ltv1 is a nuclear export adapter for the pre-40S subunit, its function must be fully redundant with additional export factors. The dominant negative phenotype of Ltv1∆NES overexpression was suppressed by co-overexpressing RpS3 and its chaperone, Yar1, or by deletion of the RpS3-binding site in Ltv1∆NES, suggesting that titration of RpS3 by Ltv1∆NES is deleterious in yeast. The dominant-negative phenotype did not correlate with a decrease in 40S levels but rather with a reduction in the polysome-to-monosome ratio, indicating reduced rates of translation. We suggest that titration of RpS3 by excess nuclear Ltv1 interferes with 40S function or with a nonribosomal function of RpS3.
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Affiliation(s)
- Jason R Merwin
- Biochemistry and Molecular Biology Program, Lewis & Clark College, Portland, Oregon 97219
| | - Lucien B Bogar
- Biochemistry and Molecular Biology Program, Lewis & Clark College, Portland, Oregon 97219
| | - Sarah B Poggi
- Biochemistry and Molecular Biology Program, Lewis & Clark College, Portland, Oregon 97219
| | - Rebecca M Fitch
- Biochemistry and Molecular Biology Program, Lewis & Clark College, Portland, Oregon 97219
| | - Arlen W Johnson
- Department of Molecular Biosciences, University of Texas, Austin, Texas 78712
| | - Deborah E Lycan
- Biochemistry and Molecular Biology Program, Lewis & Clark College, Portland, Oregon 97219
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31
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Assembly and nuclear export of pre-ribosomal particles in budding yeast. Chromosoma 2014; 123:327-44. [PMID: 24817020 DOI: 10.1007/s00412-014-0463-z] [Citation(s) in RCA: 43] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/18/2013] [Revised: 03/18/2014] [Accepted: 04/07/2014] [Indexed: 11/27/2022]
Abstract
The ribosome is responsible for the final step of decoding genetic information into proteins. Therefore, correct assembly of ribosomes is a fundamental task for all living cells. In eukaryotes, the construction of the ribosome which begins in the nucleolus requires coordinated efforts of >350 specialized factors that associate with pre-ribosomal particles at distinct stages to perform specific assembly steps. On their way through the nucleus, diverse energy-consuming enzymes are thought to release assembly factors from maturing pre-ribosomal particles after accomplishing their task(s). Subsequently, recruitment of export factors prepares pre-ribosomal particles for transport through nuclear pore complexes. Pre-ribosomes are exported into the cytoplasm in a functionally inactive state, where they undergo final maturation before initiating translation. Accumulating evidence indicates a tight coupling between nuclear export, cytoplasmic maturation, and final proofreading of the ribosome. In this review, we summarize our current understanding of nuclear export of pre-ribosomal subunits and cytoplasmic maturation steps that render pre-ribosomal subunits translation-competent.
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32
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Abstract
Construction of the eukaryotic ribosome begins in the nucleolus and requires >300 evolutionarily conserved nonribosomal trans-acting factors, which transiently associate with preribosomal subunits at distinct assembly stages. A subset of trans-acting and transport factors passage assembled preribosomal subunits in a functionally inactive state through the nuclear pore complexes (NPC) into the cytoplasm, where they undergo final maturation before initiating translation. Here, we summarize the repertoire of tools developed in the model organism budding yeast that are spearheading the functional analyses of trans-acting factors involved in the assembly and intracellular transport of preribosomal subunits. We elaborate on different GFP-tagged ribosomal protein reporters and a pre-rRNA reporter that reliably monitors the movement of preribosomal particles from the nucleolus to cytoplasm. We discuss the powerful yeast heterokaryon assay, which can be employed to uncover shuttling trans-acting factors that need to accompany preribosomal subunits to the cytoplasm to be released prior to initiating translation. Moreover, we present two biochemical approaches, namely sucrose gradient analyses and tandem affinity purification, that are rapidly facilitating the uncovering of regulatory processes that control the compositional dynamics of trans-acting factors on maturing preribosomal particles. Altogether, these approaches when combined with traditional analytical biochemistry, targeted proteomics and structural methodologies, will contribute to the dissection of the assembly and intracellular transport of preribosomal subunits, as well as other macromolecular assemblies that influence diverse biological pathways.
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MESH Headings
- Biological Transport/genetics
- Green Fluorescent Proteins/genetics
- In Situ Hybridization, Fluorescence/methods
- Karyopherins/genetics
- Mass Spectrometry/methods
- Microscopy, Fluorescence/methods
- Nuclear Pore/genetics
- Nuclear Pore/metabolism
- Nucleolus Organizer Region/genetics
- RNA, Ribosomal/biosynthesis
- RNA, Ribosomal/genetics
- Receptors, Cytoplasmic and Nuclear/genetics
- Ribosome Subunits, Large, Eukaryotic/genetics
- Ribosome Subunits, Large, Eukaryotic/metabolism
- Ribosome Subunits, Small, Eukaryotic/genetics
- Ribosome Subunits, Small, Eukaryotic/metabolism
- Saccharomyces cerevisiae/genetics
- Saccharomyces cerevisiae/metabolism
- Ultracentrifugation/methods
- Exportin 1 Protein
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Affiliation(s)
- Martin Altvater
- Institute of Biochemistry (IBC), ETH Zürich, Otto-Stern-Weg 3, Zurich, Switzerland; MLS Program, Life Science Zurich Graduate School, Winterthurerstrasse 190, Zurich, Switzerland
| | - Sabina Schütz
- Institute of Biochemistry (IBC), ETH Zürich, Otto-Stern-Weg 3, Zurich, Switzerland; MLS Program, Life Science Zurich Graduate School, Winterthurerstrasse 190, Zurich, Switzerland
| | - Yiming Chang
- Institute of Biochemistry (IBC), ETH Zürich, Otto-Stern-Weg 3, Zurich, Switzerland
| | - Vikram Govind Panse
- Institute of Biochemistry (IBC), ETH Zürich, Otto-Stern-Weg 3, Zurich, Switzerland
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33
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Woolford JL, Baserga SJ. Ribosome biogenesis in the yeast Saccharomyces cerevisiae. Genetics 2013; 195:643-81. [PMID: 24190922 PMCID: PMC3813855 DOI: 10.1534/genetics.113.153197] [Citation(s) in RCA: 558] [Impact Index Per Article: 50.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2013] [Accepted: 08/26/2013] [Indexed: 01/09/2023] Open
Abstract
Ribosomes are highly conserved ribonucleoprotein nanomachines that translate information in the genome to create the proteome in all cells. In yeast these complex particles contain four RNAs (>5400 nucleotides) and 79 different proteins. During the past 25 years, studies in yeast have led the way to understanding how these molecules are assembled into ribosomes in vivo. Assembly begins with transcription of ribosomal RNA in the nucleolus, where the RNA then undergoes complex pathways of folding, coupled with nucleotide modification, removal of spacer sequences, and binding to ribosomal proteins. More than 200 assembly factors and 76 small nucleolar RNAs transiently associate with assembling ribosomes, to enable their accurate and efficient construction. Following export of preribosomes from the nucleus to the cytoplasm, they undergo final stages of maturation before entering the pool of functioning ribosomes. Elaborate mechanisms exist to monitor the formation of correct structural and functional neighborhoods within ribosomes and to destroy preribosomes that fail to assemble properly. Studies of yeast ribosome biogenesis provide useful models for ribosomopathies, diseases in humans that result from failure to properly assemble ribosomes.
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Affiliation(s)
- John L. Woolford
- Department of Biological Sciences, Center for Nucleic Acids Science and Technology, Carnegie Mellon University, Pittsburgh, Pennsylvania 15213
| | - Susan J. Baserga
- Molecular Biophysics and Biochemistry, Genetics and Therapeutic Radiology, Yale University, New Haven, Connecticut 06520-8024
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34
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Occhipinti L, Chang Y, Altvater M, Menet AM, Kemmler S, Panse VG. Non-FG mediated transport of the large pre-ribosomal subunit through the nuclear pore complex by the mRNA export factor Gle2. Nucleic Acids Res 2013; 41:8266-79. [PMID: 23907389 PMCID: PMC3783196 DOI: 10.1093/nar/gkt675] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/19/2023] Open
Abstract
Multiple export receptors passage bound pre-ribosomes through nuclear pore complexes (NPCs) by transiently interacting with the Phe-Gly (FG) meshwork of their transport channels. Here, we reveal how the non-FG interacting yeast mRNA export factor Gly-Leu-FG lethal 2 (Gle2) functions in the export of the large pre-ribosomal subunit (pre-60S). Structure-guided studies uncovered conserved platforms used by Gle2 to export pre-60S: an uncharacterized basic patch required to bind pre-60S, and a second surface that makes non-FG contacts with the nucleoporin Nup116. A basic patch mutant of Gle2 is able to function in mRNA export, but not pre-60S export. Thus, Gle2 provides a distinct interaction platform to transport pre-60S to the cytoplasm. Notably, Gle2’s interaction platforms become crucial for pre-60S export when FG-interacting receptors are either not recruited to pre-60S or are impaired. We propose that large complex cargos rely on non-FG as well as FG-interactions for their efficient translocation through the nuclear pore complex channel.
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Affiliation(s)
- Laura Occhipinti
- Department of Biology (D-BIOL), Institute of Biochemistry (IBC), ETH Zurich, Schafmattstrasse 18, CH-8093 Zurich, Switzerland and MLS Program, Life Sciences Zurich Graduate School, Winterthurerstrasse 190, CH-8057 Zurich, Switzerland
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35
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Ohmayer U, Gamalinda M, Sauert M, Ossowski J, Pöll G, Linnemann J, Hierlmeier T, Perez-Fernandez J, Kumcuoglu B, Leger-Silvestre I, Faubladier M, Griesenbeck J, Woolford J, Tschochner H, Milkereit P. Studies on the assembly characteristics of large subunit ribosomal proteins in S. cerevisae. PLoS One 2013; 8:e68412. [PMID: 23874617 PMCID: PMC3707915 DOI: 10.1371/journal.pone.0068412] [Citation(s) in RCA: 48] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2013] [Accepted: 05/29/2013] [Indexed: 11/18/2022] Open
Abstract
During the assembly process of ribosomal subunits, their structural components, the ribosomal RNAs (rRNAs) and the ribosomal proteins (r-proteins) have to join together in a highly dynamic and defined manner to enable the efficient formation of functional ribosomes. In this work, the assembly of large ribosomal subunit (LSU) r-proteins from the eukaryote S. cerevisiae was systematically investigated. Groups of LSU r-proteins with specific assembly characteristics were detected by comparing the protein composition of affinity purified early, middle, late or mature LSU (precursor) particles by semi-quantitative mass spectrometry. The impact of yeast LSU r-proteins rpL25, rpL2, rpL43, and rpL21 on the composition of intermediate to late nuclear LSU precursors was analyzed in more detail. Effects of these proteins on the assembly states of other r-proteins and on the transient LSU precursor association of several ribosome biogenesis factors, including Nog2, Rsa4 and Nop53, are discussed.
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Affiliation(s)
- Uli Ohmayer
- Lehrstuhl für Biochemie III, Universität Regensburg, Regensburg, Germany
| | - Michael Gamalinda
- Department of Biological Sciences, Carnegie Mellon University, Pittsburgh, Pennsylvania, United States of America
| | - Martina Sauert
- Lehrstuhl für Biochemie III, Universität Regensburg, Regensburg, Germany
| | - Julius Ossowski
- Lehrstuhl für Biochemie III, Universität Regensburg, Regensburg, Germany
| | - Gisela Pöll
- Lehrstuhl für Biochemie III, Universität Regensburg, Regensburg, Germany
| | - Jan Linnemann
- Lehrstuhl für Biochemie III, Universität Regensburg, Regensburg, Germany
| | - Thomas Hierlmeier
- Lehrstuhl für Biochemie III, Universität Regensburg, Regensburg, Germany
| | | | - Beril Kumcuoglu
- Department of Biological Sciences, Carnegie Mellon University, Pittsburgh, Pennsylvania, United States of America
| | - Isabelle Leger-Silvestre
- Laboratoire de Biologie Moléculaire Eucaryote, UMR 5099, Universite Paul Sabatier, Toulouse, France
| | - Marlène Faubladier
- Laboratoire de Biologie Moléculaire Eucaryote, UMR 5099, Universite Paul Sabatier, Toulouse, France
| | | | - John Woolford
- Department of Biological Sciences, Carnegie Mellon University, Pittsburgh, Pennsylvania, United States of America
| | - Herbert Tschochner
- Lehrstuhl für Biochemie III, Universität Regensburg, Regensburg, Germany
| | - Philipp Milkereit
- Lehrstuhl für Biochemie III, Universität Regensburg, Regensburg, Germany
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36
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Targeted proteomics reveals compositional dynamics of 60S pre-ribosomes after nuclear export. Mol Syst Biol 2013; 8:628. [PMID: 23212245 PMCID: PMC3542530 DOI: 10.1038/msb.2012.63] [Citation(s) in RCA: 44] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/10/2012] [Accepted: 11/02/2012] [Indexed: 01/16/2023] Open
Abstract
Construction and intracellular targeting of eukaryotic pre-ribosomal particles involve a multitude of diverse transiently associating trans-acting assembly factors, energy-consuming enzymes, and transport factors. The ability to rapidly and reliably measure co-enrichment of multiple factors with maturing pre-ribosomal particles presents a major biochemical bottleneck towards revealing their function and the precise contribution of >50 energy-consuming steps that drive ribosome assembly. Here, we devised a workflow that combines genetic trapping, affinity-capture, and selected reaction monitoring mass spectrometry (SRM-MS), to overcome this deficiency. We exploited this approach to interrogate the dynamic proteome of pre-60S particles after nuclear export. We uncovered assembly factors that travel with pre-60S particles to the cytoplasm, where they are released before initiating translation. Notably, we identified a novel shuttling factor that facilitates nuclear export of pre-60S particles. Capturing and quantitating protein interaction networks of trapped intermediates of macromolecular complexes by our workflow is a reliable discovery tool to unveil dynamic processes that contribute to their in vivo assembly and transport.
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37
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Kappel L, Loibl M, Zisser G, Klein I, Fruhmann G, Gruber C, Unterweger S, Rechberger G, Pertschy B, Bergler H. Rlp24 activates the AAA-ATPase Drg1 to initiate cytoplasmic pre-60S maturation. ACTA ACUST UNITED AC 2013. [PMID: 23185031 PMCID: PMC3514788 DOI: 10.1083/jcb.201205021] [Citation(s) in RCA: 56] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
Formation of eukaryotic ribosomes is driven by energy-consuming enzymes. The AAA-ATPase Drg1 is essential for the release of several shuttling proteins from cytoplasmic pre-60S particles and the loading of late joining proteins. However, its exact role in ribosome biogenesis has been unknown. Here we show that the shuttling protein Rlp24 recruited Drg1 to pre-60S particles and stimulated its ATPase activity. ATP hydrolysis in the second AAA domain of Drg1 was required to release shuttling proteins. In vitro, Drg1 specifically and exclusively extracted Rlp24 from purified pre-60S particles. Rlp24 release required ATP and was promoted by the interaction of Drg1 with the nucleoporin Nup116. Subsequent ATP hydrolysis in the first AAA domain dissociated Drg1 from Rlp24, liberating both proteins for consecutive cycles of activity. Our results show that release of Rlp24 by Drg1 defines a key event in large subunit formation that is a prerequisite for progression of cytoplasmic pre-60S maturation.
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Affiliation(s)
- Lisa Kappel
- Institut für Molekulare Biowissenschaften, Karl-Franzens Universität Graz, A-8010 Graz, Austria
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38
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Karbstein K. Quality control mechanisms during ribosome maturation. Trends Cell Biol 2013; 23:242-50. [PMID: 23375955 DOI: 10.1016/j.tcb.2013.01.004] [Citation(s) in RCA: 89] [Impact Index Per Article: 8.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/08/2012] [Revised: 01/08/2013] [Accepted: 01/08/2013] [Indexed: 12/01/2022]
Abstract
Protein synthesis on ribosomes is carefully quality-controlled to ensure the faithful transmission of genetic information from mRNA to protein. Many of these mechanisms rely on communication between distant sites on the ribosomes, and thus on the integrity of the ribosome structure. Furthermore, haploinsufficiency of ribosomal proteins, which increases the chances of forming incompletely assembled ribosomes, can predispose to cancer. Finally, release of inactive ribosomes into the translating pool will lead to their degradation together with the degradation of the bound mRNA. Together, these findings suggest that quality control mechanisms must be in place to survey nascent ribosomes and ensure their functionality. This review gives an account of these mechanisms as currently known.
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Affiliation(s)
- Katrin Karbstein
- Department of Cancer Biology, The Scripps Research Institute, 130 Scripps Way #2C2, Jupiter, FL 33458, USA.
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Baßler J, Klein I, Schmidt C, Kallas M, Thomson E, Wagner MA, Bradatsch B, Rechberger G, Strohmaier H, Hurt E, Bergler H. The conserved Bud20 zinc finger protein is a new component of the ribosomal 60S subunit export machinery. Mol Cell Biol 2012; 32:4898-912. [PMID: 23045392 PMCID: PMC3510546 DOI: 10.1128/mcb.00910-12] [Citation(s) in RCA: 36] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2012] [Accepted: 09/17/2012] [Indexed: 01/03/2023] Open
Abstract
The nuclear export of the preribosomal 60S (pre-60S) subunit is coordinated with late steps in ribosome assembly. Here, we show that Bud20, a conserved C(2)H(2)-type zinc finger protein, is an unrecognized shuttling factor required for the efficient export of pre-60S subunits. Bud20 associates with late pre-60S particles in the nucleoplasm and accompanies them into the cytoplasm, where it is released through the action of the Drg1 AAA-ATPase. Cytoplasmic Bud20 is then reimported via a Kap123-dependent pathway. The deletion of Bud20 induces a strong pre-60S export defect and causes synthetic lethality when combined with mutant alleles of known pre-60S subunit export factors. The function of Bud20 in ribosome export depends on a short conserved N-terminal sequence, as we observed that mutations or the deletion of this motif impaired 60S subunit export and generated the genetic link to other pre-60S export factors. We suggest that the shuttling Bud20 is recruited to the nascent 60S subunit via its central zinc finger rRNA binding domain to facilitate the subsequent nuclear export of the preribosome employing its N-terminal extension.
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MESH Headings
- Active Transport, Cell Nucleus
- Amino Acid Sequence
- Gene Deletion
- Genes, Fungal
- Models, Biological
- Models, Molecular
- Molecular Sequence Data
- Mutant Proteins/genetics
- Mutant Proteins/metabolism
- Mutation
- Protein Conformation
- RNA-Binding Proteins/chemistry
- RNA-Binding Proteins/genetics
- RNA-Binding Proteins/metabolism
- Ribosomal Proteins/chemistry
- Ribosomal Proteins/genetics
- Ribosomal Proteins/metabolism
- Ribosome Subunits, Large, Eukaryotic/chemistry
- Ribosome Subunits, Large, Eukaryotic/genetics
- Ribosome Subunits, Large, Eukaryotic/metabolism
- Saccharomyces cerevisiae/genetics
- Saccharomyces cerevisiae/metabolism
- Saccharomyces cerevisiae Proteins/chemistry
- Saccharomyces cerevisiae Proteins/genetics
- Saccharomyces cerevisiae Proteins/metabolism
- Sequence Homology, Amino Acid
- Zinc Fingers
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Affiliation(s)
- Jochen Baßler
- Biochemie-Zentrum der Universität Heidelberg, Heidelberg, Germany
| | - Isabella Klein
- Institut für Molekulare Biowissenschaften, Karl-Franzens Universität Graz, Graz, Austria
| | - Claudia Schmidt
- Institut für Molekulare Biowissenschaften, Karl-Franzens Universität Graz, Graz, Austria
| | - Martina Kallas
- Biochemie-Zentrum der Universität Heidelberg, Heidelberg, Germany
| | - Emma Thomson
- Biochemie-Zentrum der Universität Heidelberg, Heidelberg, Germany
| | - Maria Anna Wagner
- Institut für Molekulare Biowissenschaften, Karl-Franzens Universität Graz, Graz, Austria
| | | | - Gerald Rechberger
- Institut für Molekulare Biowissenschaften, Karl-Franzens Universität Graz, Graz, Austria
| | - Heimo Strohmaier
- Zentrum für Medizinische Grundlagenforschung, Medizinische Universität Graz, Graz, Austria
| | - Ed Hurt
- Biochemie-Zentrum der Universität Heidelberg, Heidelberg, Germany
| | - Helmut Bergler
- Institut für Molekulare Biowissenschaften, Karl-Franzens Universität Graz, Graz, Austria
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40
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Bradatsch B, Leidig C, Granneman S, Gnädig M, Tollervey D, Böttcher B, Beckmann R, Hurt E. Structure of the pre-60S ribosomal subunit with nuclear export factor Arx1 bound at the exit tunnel. Nat Struct Mol Biol 2012; 19:1234-41. [PMID: 23142978 PMCID: PMC3678077 DOI: 10.1038/nsmb.2438] [Citation(s) in RCA: 96] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/03/2012] [Accepted: 10/09/2012] [Indexed: 12/24/2022]
Abstract
Preribosomal particles evolve in the nucleus through transient interaction with biogenesis factors before export to the cytoplasm. Here, we report the architecture of the late pre-60S particle, purified from Saccharomyces cerevisiae, through Arx1, a nuclear export factor with structural homology to methionine aminopeptidases, or its binding partner Alb1. Cryo-EM reconstruction of the Arx1 particle at 11.9-Å resolution reveals regions of extra density on the pre-60S particle attributed to associated biogenesis factors, confirming the immature state of the nascent subunit. One of these densities could be unambiguously assigned to Arx1. Immunoelectron microscopy and UV cross-linking localize Arx1 close to the ribosomal exit tunnel, in direct contact with ES27, a highly dynamic eukaryotic rRNA expansion segment. The binding of Arx1 at the exit tunnel may position this export factor to prevent premature recruitment of ribosome-associated factors active during translation.
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41
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Greber BJ, Boehringer D, Montellese C, Ban N. Cryo-EM structures of Arx1 and maturation factors Rei1 and Jjj1 bound to the 60S ribosomal subunit. Nat Struct Mol Biol 2012; 19:1228-33. [PMID: 23142985 DOI: 10.1038/nsmb.2425] [Citation(s) in RCA: 84] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2012] [Accepted: 09/24/2012] [Indexed: 11/09/2022]
Abstract
Eukaryotic ribosome biogenesis requires many protein factors that facilitate the assembly, nuclear export and final maturation of 40S and 60S particles. We have biochemically characterized ribosomal complexes of the yeast 60S-biogenesis factor Arx1 and late-maturation factors Rei1 and Jjj1 and determined their cryo-EM structures. Arx1 was visualized bound to the 60S subunit together with Rei1, at 8.1-Å resolution, to reveal the molecular details of Arx1 binding whereby Arx1 arrests the eukaryotic-specific rRNA expansion segment 27 near the polypeptide tunnel exit. Rei1 and Jjj1, which have been implicated in Arx1 recycling, bind in the vicinity of Arx1 and form a network of interactions. We suggest that, in addition to the role of Arx1 during pre-60S nuclear export, the binding of Arx1 conformationally locks the pre-60S subunit and inhibits the premature association of nascent chain-processing factors to the polypeptide tunnel exit.
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Affiliation(s)
- Basil J Greber
- Institute of Molecular Biology and Biophysics, Eidgenössische Technische Hochschule (ETH) Zürich, Zürich, Switzerland
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Fernández-Pevida A, Rodríguez-Galán O, Díaz-Quintana A, Kressler D, de la Cruz J. Yeast ribosomal protein L40 assembles late into precursor 60 S ribosomes and is required for their cytoplasmic maturation. J Biol Chem 2012; 287:38390-407. [PMID: 22995916 DOI: 10.1074/jbc.m112.400564] [Citation(s) in RCA: 38] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
Most ribosomal proteins play important roles in ribosome biogenesis and function. Here, we have examined the contribution of the essential ribosomal protein L40 in these processes in the yeast Saccharomyces cerevisiae. Deletion of either the RPL40A or RPL40B gene and in vivo depletion of L40 impair 60 S ribosomal subunit biogenesis. Polysome profile analyses reveal the accumulation of half-mers and a moderate reduction in free 60 S ribosomal subunits. Pulse-chase, Northern blotting, and primer extension analyses in the L40-depleted strain clearly indicate that L40 is not strictly required for the precursor rRNA (pre-rRNA) processing reactions but contributes to optimal 27 SB pre-rRNA maturation. Moreover, depletion of L40 hinders the nucleo-cytoplasmic export of pre-60 S ribosomal particles. Importantly, all these defects most likely appear as the direct consequence of impaired Nmd3 and Rlp24 release from cytoplasmic pre-60 S ribosomal subunits and their inefficient recycling back into the nucle(ol)us. In agreement, we show that hemagglutinin epitope-tagged L40A assembles in the cytoplasm into almost mature pre-60 S ribosomal particles. Finally, we have identified that the hemagglutinin epitope-tagged L40A confers resistance to sordarin, a translation inhibitor that impairs the function of eukaryotic elongation factor 2, whereas the rpl40a and rpl40b null mutants are hypersensitive to this antibiotic. We conclude that L40 is assembled at a very late stage into pre-60 S ribosomal subunits and that its incorporation into 60 S ribosomal subunits is a prerequisite for subunit joining and may ensure proper functioning of the translocation process.
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Faza MB, Chang Y, Occhipinti L, Kemmler S, Panse VG. Role of Mex67-Mtr2 in the nuclear export of 40S pre-ribosomes. PLoS Genet 2012; 8:e1002915. [PMID: 22956913 PMCID: PMC3431309 DOI: 10.1371/journal.pgen.1002915] [Citation(s) in RCA: 55] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/07/2012] [Accepted: 07/02/2012] [Indexed: 11/19/2022] Open
Abstract
Nuclear export of mRNAs and pre-ribosomal subunits (pre40S and pre60S) is fundamental to all eukaryotes. While genetic approaches in budding yeast have identified bona fide export factors for mRNAs and pre60S subunits, little is known regarding nuclear export of pre40S subunits. The yeast heterodimeric transport receptor Mex67-Mtr2 (TAP-p15 in humans) binds mRNAs and pre60S subunits in the nucleus and facilitates their passage through the nuclear pore complex (NPC) into the cytoplasm by interacting with Phe-Gly (FG)-rich nucleoporins that line its transport channel. By exploiting a combination of genetic, cell-biological, and biochemical approaches, we uncovered an unanticipated role of Mex67-Mtr2 in the nuclear export of 40S pre-ribosomes. We show that recruitment of Mex67-Mtr2 to pre40S subunits requires loops emanating from its NTF2-like domains and that the C-terminal FG-rich nucleoporin interacting UBA-like domain within Mex67 contributes to the transport of pre40S subunits to the cytoplasm. Remarkably, the same loops also recruit Mex67-Mtr2 to pre60S subunits and to the Nup84 complex, the respective interactions crucial for nuclear export of pre60S subunits and mRNAs. Thus Mex67-Mtr2 is a unique transport receptor that employs a common interaction surface to participate in the nuclear export of both pre-ribosomal subunits and mRNAs. Mex67-Mtr2 could engage a regulatory crosstalk among the three major export pathways for optimal cellular growth and proliferation.
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Affiliation(s)
- Marius B. Faza
- Institute of Biochemistry (IBC), ETH Zurich, Zurich, Switzerland
- MLS Program, Life Science Zurich Graduate School, Zurich, Switzerland
| | - Yiming Chang
- Institute of Biochemistry (IBC), ETH Zurich, Zurich, Switzerland
| | - Laura Occhipinti
- Institute of Biochemistry (IBC), ETH Zurich, Zurich, Switzerland
- MLS Program, Life Science Zurich Graduate School, Zurich, Switzerland
| | - Stefan Kemmler
- Institute of Biochemistry (IBC), ETH Zurich, Zurich, Switzerland
| | - Vikram G. Panse
- Institute of Biochemistry (IBC), ETH Zurich, Zurich, Switzerland
- * E-mail:
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44
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Abstract
Exchange of macromolecules between the nucleus and cytoplasm is a key regulatory event in the expression of a cell's genome. This exchange requires a dedicated transport system: (1) nuclear pore complexes (NPCs), embedded in the nuclear envelope and composed of proteins termed nucleoporins (or "Nups"), and (2) nuclear transport factors that recognize the cargoes to be transported and ferry them across the NPCs. This transport is regulated at multiple levels, and the NPC itself also plays a key regulatory role in gene expression by influencing nuclear architecture and acting as a point of control for various nuclear processes. Here we summarize how the yeast Saccharomyces has been used extensively as a model system to understand the fundamental and highly conserved features of this transport system, revealing the structure and function of the NPC; the NPC's role in the regulation of gene expression; and the interactions of transport factors with their cargoes, regulatory factors, and specific nucleoporins.
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45
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The mRNA export factor Npl3 mediates the nuclear export of large ribosomal subunits. EMBO Rep 2011; 12:1024-31. [PMID: 21852791 DOI: 10.1038/embor.2011.155] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/09/2010] [Revised: 06/21/2011] [Accepted: 06/28/2011] [Indexed: 12/27/2022] Open
Abstract
The nuclear export of large ribonucleoparticles is complex and requires specific transport factors. Messenger RNAs are exported through the RNA-binding protein Npl3 and the interacting export receptor Mex67. Export of large ribosomal subunits also requires Mex67; however, in this case, Mex67 binds directly to the 5S ribosomal RNA (rRNA) and does not require the Npl3 adaptor. Here, we have discovered a new function of Npl3 in mediating the export of pre-60S ribosomal subunit independently of Mex67. Npl3 interacts with the 25S rRNA, ribosomal and ribosome-associated proteins, as well as with the nuclear pore complex. Mutations in NPL3 lead to export defects of the large subunit and genetic interactions with other pre-60S export factors.
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Kutuzov MA, Andreeva AV. Prediction of biological functions of Shewanella-like protein phosphatases (Shelphs) across different domains of life. Funct Integr Genomics 2011; 12:11-23. [DOI: 10.1007/s10142-011-0254-z] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/05/2011] [Revised: 09/07/2011] [Accepted: 09/13/2011] [Indexed: 12/12/2022]
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47
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Ran-dependent nuclear export mediators: a structural perspective. EMBO J 2011; 30:3457-74. [PMID: 21878989 DOI: 10.1038/emboj.2011.287] [Citation(s) in RCA: 159] [Impact Index Per Article: 12.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2011] [Accepted: 07/22/2011] [Indexed: 12/25/2022] Open
Abstract
Nuclear export is an essential eukaryotic activity. It proceeds through nuclear pore complexes (NPCs) and is mediated by soluble receptors that shuttle between nucleus and cytoplasm. RanGTPase-dependent export mediators (exportins) constitute the largest class of these carriers and are functionally highly versatile. All of these exportins load their substrates in response to RanGTP binding in the nucleus and traverse NPCs as ternary RanGTP-exportin-cargo complexes to the cytoplasm, where GTP hydrolysis leads to export complex disassembly. The different exportins vary greatly in their substrate range. Recent structural studies of both protein- and RNA-specific exporters have illuminated how exportins bind their cargoes, how Ran triggers cargo loading and how export complexes are disassembled in the cytoplasm. Here, we review the current state of knowledge and highlight emerging principles as well as prevailing questions.
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48
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Comparative genomics of proteins involved in RNA nucleocytoplasmic export. BMC Evol Biol 2011; 11:7. [PMID: 21223572 PMCID: PMC3032688 DOI: 10.1186/1471-2148-11-7] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2009] [Accepted: 01/11/2011] [Indexed: 12/18/2022] Open
Abstract
Background The establishment of the nuclear membrane resulted in the physical separation of transcription and translation, and presented early eukaryotes with a formidable challenge: how to shuttle RNA from the nucleus to the locus of protein synthesis. In prokaryotes, mRNA is translated as it is being synthesized, whereas in eukaryotes mRNA is synthesized and processed in the nucleus, and it is then exported to the cytoplasm. In metazoa and fungi, the different RNA species are exported from the nucleus by specialized pathways. For example, tRNA is exported by exportin-t in a RanGTP-dependent fashion. By contrast, mRNAs are associated to ribonucleoproteins (RNPs) and exported by an essential shuttling complex (TAP-p15 in human, Mex67-mtr2 in yeast) that transports them through the nuclear pore. The different RNA export pathways appear to be well conserved among members of Opisthokonta, the eukaryotic supergroup that includes Fungi and Metazoa. However, it is not known whether RNA export in the other eukaryotic supergroups follows the same export routes as in opisthokonts. Methods Our objective was to reconstruct the evolutionary history of the different RNA export pathways across eukaryotes. To do so, we screened an array of eukaryotic genomes for the presence of homologs of the proteins involved in RNA export in Metazoa and Fungi, using human and yeast proteins as queries. Results Our genomic comparisons indicate that the basic components of the RanGTP-dependent RNA pathways are conserved across eukaryotes, and thus we infer that these are traceable to the last eukaryotic common ancestor (LECA). On the other hand, several of the proteins involved in RanGTP-independent mRNA export pathways are less conserved, which would suggest that they represent innovations that appeared later in the evolution of eukaryotes. Conclusions Our analyses suggest that the LECA possessed the basic components of the different RNA export mechanisms found today in opisthokonts, and that these mechanisms became more specialized throughout eukaryotic evolution.
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Wild T, Horvath P, Wyler E, Widmann B, Badertscher L, Zemp I, Kozak K, Csucs G, Lund E, Kutay U. A protein inventory of human ribosome biogenesis reveals an essential function of exportin 5 in 60S subunit export. PLoS Biol 2010; 8:e1000522. [PMID: 21048991 PMCID: PMC2964341 DOI: 10.1371/journal.pbio.1000522] [Citation(s) in RCA: 154] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/07/2010] [Accepted: 09/03/2010] [Indexed: 12/20/2022] Open
Abstract
The assembly of ribosomal subunits in eukaryotes is a complex, multistep process so far mostly studied in yeast. In S. cerevisiae, more than 200 factors including ribosomal proteins and trans-acting factors are required for the ordered assembly of 40S and 60S ribosomal subunits. To date, only few human homologs of these yeast ribosome synthesis factors have been characterized. Here, we used a systematic RNA interference (RNAi) approach to analyze the contribution of 464 candidate factors to ribosomal subunit biogenesis in human cells. The screen was based on visual readouts, using inducible, fluorescent ribosomal proteins as reporters. By performing computer-based image analysis utilizing supervised machine-learning techniques, we obtained evidence for a functional link of 153 human proteins to ribosome synthesis. Our data show that core features of ribosome assembly are conserved from yeast to human, but differences exist for instance with respect to 60S subunit export. Unexpectedly, our RNAi screen uncovered a requirement for the export receptor Exportin 5 (Exp5) in nuclear export of 60S subunits in human cells. We show that Exp5, like the known 60S exportin Crm1, binds to pre-60S particles in a RanGTP-dependent manner. Interference with either Exp5 or Crm1 function blocks 60S export in both human cells and frog oocytes, whereas 40S export is compromised only upon inhibition of Crm1. Thus, 60S subunit export is dependent on at least two RanGTP-binding exportins in vertebrate cells.
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Affiliation(s)
- Thomas Wild
- Institute of Biochemistry, ETH Zurich, Zurich, Switzerland
- Molecular Life Science Ph.D. Program, Zurich, Switzerland
| | - Peter Horvath
- Light Microscopy Center, RISC, Department of Biology, ETH Zurich, Zurich, Switzerland
| | - Emanuel Wyler
- Institute of Biochemistry, ETH Zurich, Zurich, Switzerland
- Molecular Life Science Ph.D. Program, Zurich, Switzerland
| | - Barbara Widmann
- Institute of Biochemistry, ETH Zurich, Zurich, Switzerland
- Molecular Life Science Ph.D. Program, Zurich, Switzerland
| | - Lukas Badertscher
- Institute of Biochemistry, ETH Zurich, Zurich, Switzerland
- Molecular Life Science Ph.D. Program, Zurich, Switzerland
| | - Ivo Zemp
- Institute of Biochemistry, ETH Zurich, Zurich, Switzerland
| | - Karol Kozak
- Light Microscopy Center, RISC, Department of Biology, ETH Zurich, Zurich, Switzerland
| | - Gabor Csucs
- Light Microscopy Center, RISC, Department of Biology, ETH Zurich, Zurich, Switzerland
| | - Elsebet Lund
- University of Wisconsin, Madison, Wisconsin, United States of America
| | - Ulrike Kutay
- Institute of Biochemistry, ETH Zurich, Zurich, Switzerland
- * E-mail:
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50
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Sengupta J, Bussiere C, Pallesen J, West M, Johnson AW, Frank J. Characterization of the nuclear export adaptor protein Nmd3 in association with the 60S ribosomal subunit. ACTA ACUST UNITED AC 2010; 189:1079-86. [PMID: 20584915 PMCID: PMC2894450 DOI: 10.1083/jcb.201001124] [Citation(s) in RCA: 53] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/10/2023]
Abstract
The nucleocytoplasmic shuttling protein Nmd3 is an adaptor for export of the 60S ribosomal subunit from the nucleus. Nmd3 binds to nascent 60S subunits in the nucleus and recruits the export receptor Crm1 to facilitate passage through the nuclear pore complex. In this study, we present a cryoelectron microscopy (cryo-EM) reconstruction of the 60S subunit in complex with Nmd3 from Saccharomyces cerevisiae. The density corresponding to Nmd3 is directly visible in the cryo-EM map and is attached to the regions around helices 38, 69, and 95 of the 25S ribosomal RNA (rRNA), the helix 95 region being adjacent to the protein Rpl10. We identify the intersubunit side of the large subunit as the binding site for Nmd3. rRNA protection experiments corroborate the structural data. Furthermore, Nmd3 binding to 60S subunits is blocked in 80S ribosomes, which is consistent with the assigned binding site on the subunit joining face. This cryo-EM map is a first step toward a molecular understanding of the functional role and release mechanism of Nmd3.
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Affiliation(s)
- Jayati Sengupta
- Wadsworth Center, New York State Department of Health, Albany, NY 12201, USA
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