1
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Dziurdzik SK, Bean BDM, Davey M, Conibear E. A VPS13D spastic ataxia mutation disrupts the conserved adaptor-binding site in yeast Vps13. Hum Mol Genet 2021; 29:635-648. [PMID: 31943017 PMCID: PMC7068118 DOI: 10.1093/hmg/ddz318] [Citation(s) in RCA: 30] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/13/2019] [Revised: 12/19/2019] [Accepted: 12/27/2019] [Indexed: 12/12/2022] Open
Abstract
Mutations in each of the four human VPS13 (VPS13A-D) proteins are associated with distinct neurological disorders: chorea-acanthocytosis, Cohen syndrome, early-onset Parkinson's disease and spastic ataxia. Recent evidence suggests that the different VPS13 paralogs transport lipids between organelles at different membrane contact sites. How each VPS13 isoform is targeted to organelles is not known. We have shown that the localization of yeast Vps13 protein to membranes requires a conserved six-repeat region, the Vps13 Adaptor Binding (VAB) domain, which binds to organelle-specific adaptors. Here, we use a systematic mutagenesis strategy to determine the role of each repeat in recognizing each known adaptor. Our results show that mutation of invariant asparagines in repeats 1 and 6 strongly impacts the binding of all adaptors and blocks Vps13 membrane recruitment. However, we find that repeats 5-6 are sufficient for localization and interaction with adaptors. This supports a model where a single adaptor-binding site is found in the last two repeats of the VAB domain, while VAB domain repeat 1 may influence domain conformation. Importantly, a disease-causing mutation in VPS13D, which maps to the highly conserved asparagine residue in repeat 6, blocks adaptor binding and Vps13 membrane recruitment when modeled in yeast. Our findings are consistent with a conserved adaptor binding role for the VAB domain and suggest the presence of as-yet-unidentified adaptors in both yeast and humans.
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Affiliation(s)
- Samantha K Dziurdzik
- Centre for Molecular Medicine and Therapeutics, British Columbia Children's Hospital Research Institute, University of British Columbia, Vancouver, BC V5Z 4H4, Canada.,Department of Medical Genetics, University of British Columbia, Vancouver, BC V6H 3N1, Canada
| | - Björn D M Bean
- Department of Biology, Concordia University, Montreal, QC H3G 1M8, Canada
| | - Michael Davey
- Centre for Molecular Medicine and Therapeutics, British Columbia Children's Hospital Research Institute, University of British Columbia, Vancouver, BC V5Z 4H4, Canada
| | - Elizabeth Conibear
- Centre for Molecular Medicine and Therapeutics, British Columbia Children's Hospital Research Institute, University of British Columbia, Vancouver, BC V5Z 4H4, Canada.,Department of Medical Genetics, University of British Columbia, Vancouver, BC V6H 3N1, Canada
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2
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Wei L, Li P, Luo Y, Zhang M, Yan T, Yang Y, Han Y, Liu S, Wang E. PWP1 Promotes the Malignant Phenotypes of Lung Cancer Cells by Interacting with DVL2 and Merlin. Onco Targets Ther 2020; 13:10025-10037. [PMID: 33116587 PMCID: PMC7553635 DOI: 10.2147/ott.s263815] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/02/2020] [Accepted: 09/15/2020] [Indexed: 11/23/2022] Open
Abstract
Purpose The significance of periodic tryptophan protein 1 (PWP1) expression in human cancer and its molecular mechanism of action have not been reported so far. Materials and Methods Immunohistochemistry was performed to analyze the expression of PWP1 in non-small cell lung cancer (NSCLC) tissues and statistical analysis was applied to analyze the relationship between PWP1 expression and the clinicopathological factors. The effects of PWP1 on NSCLC proliferation and invasion were determined by colony formation, transwell and MTT assays. Western blot analysis (WB), dual-luciferase reporter gene assays and immunofluorescence staining were performed to demonstrate whether PWP1 stimulates Wnt pathway and inhibits Hippo pathway. Co-immunoprecipitation (Co-ip) assays were used to confirm the potential role of PWP1 in Wnt and Hippo signaling pathways. Results PWP1 expression in NSCLC was higher than that in normal bronchial epithelium and normal submucosal glands. In addition, PWP1 expression had a positive correlation with poor differentiation, high pathological tumor-node-metastasis (TNM) stage, and lymph node metastasis. Kaplan–Meier database demonstrated that the overall survival time of patients with high PWP1 expression was significantly shorter than that of patients with low PWP1 expression. Mechanistically, we found that PWP1 could interact with DVL2 to upregulate β-catenin (thereby activating the Wnt pathway), whereas PWP1 could interact with Merlin (NF2) to downregulate p-MST1 (thereby inhibiting the Hippo signaling pathway). The effects of PWP1 on promoting the Wnt pathway or inhibiting the Hippo pathway were offset in DVL2- or Merlin-knockdown cells transiently overexpressing PWP1. Conclusion PWP1 expression in NSCLC was correlated with poor prognosis. PWP1 enhanced the activity of the Wnt pathway by interacting with DVL2, whereas PWP1 inhibited the activity of the Hippo pathway by interacting with Merlin. Together, these two effects promoted the detrimental biological behaviors of NSCLC cells.
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Affiliation(s)
- Lai Wei
- Department of Pathology, College of Basic Medical Science, and First Affiliated Hospital of China Medical University, Shenyang, People's Republic of China
| | - Pengcheng Li
- Department of Pathology, College of Basic Medical Science, and First Affiliated Hospital of China Medical University, Shenyang, People's Republic of China
| | - Yuan Luo
- Department of Pathology, College of Basic Medical Science, and First Affiliated Hospital of China Medical University, Shenyang, People's Republic of China
| | - Meiyu Zhang
- Department of Pathology, College of Basic Medical Science, and First Affiliated Hospital of China Medical University, Shenyang, People's Republic of China
| | - Ting Yan
- Department of Pathology, College of Basic Medical Science, and First Affiliated Hospital of China Medical University, Shenyang, People's Republic of China
| | - Yue Yang
- Department of Pathology, College of Basic Medical Science, and First Affiliated Hospital of China Medical University, Shenyang, People's Republic of China
| | - Yuchen Han
- Department of Pathology, Shanghai Chest Hospital, Shanghai Jiao Tong University, Shanghai, People's Republic of China
| | - Shuli Liu
- Department of Pathology, College of Basic Medical Science, and First Affiliated Hospital of China Medical University, Shenyang, People's Republic of China
| | - Enhua Wang
- Department of Pathology, College of Basic Medical Science, and First Affiliated Hospital of China Medical University, Shenyang, People's Republic of China
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3
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Clerget G, Bourguignon-Igel V, Marmier-Gourrier N, Rolland N, Wacheul L, Manival X, Charron C, Kufel J, Méreau A, Senty-Ségault V, Tollervey D, Lafontaine DLJ, Branlant C, Rederstorff M. Synergistic defects in pre-rRNA processing from mutations in the U3-specific protein Rrp9 and U3 snoRNA. Nucleic Acids Res 2020; 48:3848-3868. [PMID: 31996908 PMCID: PMC7144924 DOI: 10.1093/nar/gkaa066] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2019] [Revised: 01/17/2020] [Accepted: 01/22/2020] [Indexed: 01/24/2023] Open
Abstract
U3 snoRNA and the associated Rrp9/U3-55K protein are essential for 18S rRNA production by the SSU-processome complex. U3 and Rrp9 are required for early pre-rRNA cleavages at sites A0, A1 and A2, but the mechanism remains unclear. Substitution of Arg 289 in Rrp9 to Ala (R289A) specifically reduced cleavage at sites A1 and A2. Surprisingly, R289 is located on the surface of the Rrp9 β-propeller structure opposite to U3 snoRNA. To understand this, we first characterized the protein-protein interaction network of Rrp9 within the SSU-processome. This identified a direct interaction between the Rrp9 β-propeller domain and Rrp36, the strength of which was reduced by the R289A substitution, implicating this interaction in the observed processing phenotype. The Rrp9 R289A mutation also showed strong synergistic negative interactions with mutations in U3 that destabilize the U3/pre-rRNA base-pair interactions or reduce the length of their linking segments. We propose that the Rrp9 β-propeller and U3/pre-rRNA binding cooperate in the structure or stability of the SSU-processome. Additionally, our analysis of U3 variants gave insights into the function of individual segments of the 5′-terminal 72-nt sequence of U3. We interpret these data in the light of recently reported SSU-processome structures.
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Affiliation(s)
| | | | | | | | - Ludivine Wacheul
- RNA Molecular Biology, Fonds de la Recherche Scientifique (F.R.S/FNRS), Université Libre de Bruxelles (ULB), and Center for Microscopy and Molecular Imaging (CMMI), B-6041 Charleroi-Gosselies, Belgium
| | - Xavier Manival
- Université de Lorraine, CNRS, IMoPA, F-54000 Nancy, France
| | | | - Joanna Kufel
- Wellcome Center for Cell Biology, University of Edinburgh, Scotland, UK
| | - Agnès Méreau
- Université de Lorraine, CNRS, IMoPA, F-54000 Nancy, France
| | | | - David Tollervey
- Wellcome Center for Cell Biology, University of Edinburgh, Scotland, UK
| | - Denis L J Lafontaine
- RNA Molecular Biology, Fonds de la Recherche Scientifique (F.R.S/FNRS), Université Libre de Bruxelles (ULB), and Center for Microscopy and Molecular Imaging (CMMI), B-6041 Charleroi-Gosselies, Belgium
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4
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Abstract
In the past 25 years, genetic and biochemical analyses of ribosome assembly in yeast have identified most of the factors that participate in this complex pathway and have generated models for the mechanisms driving the assembly. More recently, the publication of numerous cryo-electron microscopy structures of yeast ribosome assembly intermediates has provided near-atomic resolution snapshots of ribosome precursor particles. Satisfyingly, these structural data support the genetic and biochemical models and provide additional mechanistic insight into ribosome assembly. In this Review, we discuss the mechanisms of assembly of the yeast small ribosomal subunit and large ribosomal subunit in the nucleolus, nucleus and cytoplasm. Particular emphasis is placed on concepts such as the mechanisms of RNA compaction, the functions of molecular switches and molecular mimicry, the irreversibility of assembly checkpoints and the roles of structural and functional proofreading of pre-ribosomal particles.
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5
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Shu S, Ye K. Structural and functional analysis of ribosome assembly factor Efg1. Nucleic Acids Res 2019; 46:2096-2106. [PMID: 29361028 PMCID: PMC5829643 DOI: 10.1093/nar/gky011] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/11/2017] [Accepted: 01/06/2018] [Indexed: 11/23/2022] Open
Abstract
Ribosome biogenesis in eukaryotes is a complicated process that involves association and dissociation of numerous assembly factors and snoRNAs. The yeast small ribosomal subunit is first assembled into 90S pre-ribosomes in an ordered and dynamic manner. Efg1 is a protein with no recognizable domain that is associated with early 90S particles. Here, we determine the crystal structure of Efg1 from Chaetomium thermophilum at 3.3 Å resolution, revealing a novel elongated all-helical structure. Efg1 is not located in recently determined cryo-EM densities of 90S likely due to its low abundance in mature 90S. Genetic analysis in Saccharomyces cerevisiae shows that the functional core of Efg1 contains two helical hairpins composed of highly conserved residues. Depletion of Efg1 blocks 18S rRNA processing at sites A1 and A2, but not at site A0, and production of small ribosomal subunits. Efg1 is initially recruited by the 5′ domain of 18S rRNA. Its absence disturbs the assembly of the 5′ domain and inhibits release of U14 snoRNA from 90S. Our study shows that Efg1 is required for early assembly and reorganization of the 5′ domain of 18S rRNA.
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Affiliation(s)
- Sheng Shu
- Graduate School of Peking Union Medical College and Chinese Academy of Medical Sciences, Beijing 100730, China.,National Institute of Biological Sciences, Beijing 102206, China.,Key Laboratory of RNA Biology, CAS Center for Excellence in Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing 100101, China
| | - Keqiong Ye
- Graduate School of Peking Union Medical College and Chinese Academy of Medical Sciences, Beijing 100730, China.,Key Laboratory of RNA Biology, CAS Center for Excellence in Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing 100101, China.,University of Chinese Academy of Sciences, Beijing 100049, China
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6
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Assembly and structure of the SSU processome-a nucleolar precursor of the small ribosomal subunit. Curr Opin Struct Biol 2018; 49:85-93. [PMID: 29414516 DOI: 10.1016/j.sbi.2018.01.008] [Citation(s) in RCA: 56] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/11/2017] [Revised: 01/11/2018] [Accepted: 01/12/2018] [Indexed: 12/22/2022]
Abstract
The small subunit processome is the first precursor of the small eukaryotic ribosomal subunit. During its assembly in the nucleolus, many ribosome biogenesis factors, an RNA chaperone, and ribosomal proteins associate with the nascent pre-rRNA. Biochemical studies have elucidated the rRNA-subdomain dependent recruitment of these factors during SSU processome assembly and have been complemented by structural studies of the assembled particle. Ribosome biogenesis factors encapsulate and guide subdomains of pre-ribosomal RNA in distinct compartments. This prevents uncoordinated maturation and enables processing of regions not accessible in the mature subunit. By sequentially reducing conformational freedom, flexible proteins facilitate the incorporation of dynamic subcomplexes into a globular particle. Large rearrangements within the SSU processome are required for compaction into the mature small ribosomal subunit.
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7
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Kobayashi M, Jitoku D, Iwayama Y, Yamamoto N, Toyota T, Suzuki K, Kikuchi M, Hashimoto T, Kanahara N, Kurumaji A, Yoshikawa T, Nishikawa T. Association studies of WD repeat domain 3 and chitobiosyldiphosphodolichol beta-mannosyltransferase genes with schizophrenia in a Japanese population. PLoS One 2018; 13:e0190991. [PMID: 29309433 PMCID: PMC5757935 DOI: 10.1371/journal.pone.0190991] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/09/2017] [Accepted: 12/22/2017] [Indexed: 12/03/2022] Open
Abstract
Schizophrenia and schizophrenia-like symptoms induced by the dopamine agonists and N-methyl-D aspartate type glutamate receptor antagonists occur only after the adolescent period. Similarly, animal models of schizophrenia by these drugs are also induced after the critical period around postnatal week three. Based upon the development-dependent onsets of these psychotomimetic effects, by using a DNA microarray technique, we identified the WD repeat domain 3 (WDR3) and chitobiosyldiphosphodolichol beta-mannosyltransferase (ALG1) genes as novel candidates for schizophrenia-related molecules, whose mRNAs were up-regulated in the adult (postnatal week seven), but not in the infant (postnatal week one) rats by an indirect dopamine agonist, and phencyclidine, an antagonist of the NMDA receptor. WDR3 and other related proteins are the nuclear proteins presumably involved in various cellular activities, such as cell cycle progression, signal transduction, apoptosis, and gene regulation. ALG1 is presumed to be involved in the regulation of the protein N-glycosylation. To further elucidate the molecular pathophysiology of schizophrenia, we have evaluated the genetic association of WDR3 and ALG1 in schizophrenia. We examined 21 single nucleotide polymorphisms [SNPs; W1 (rs1812607)-W16 (rs6656360), A1 (rs8053916)-A10 (rs9673733)] from these genes using the Japanese case-control sample (1,808 schizophrenics and 2,170 matched controls). No significant genetic associations of these SNPs were identified. However, we detected a significant association of W4 (rs319471) in the female schizophrenics (allelic P = 0.003, genotypic P = 0.008). Based on a haplotype analysis, the observed haplotypes consisting of W4 (rs319471)–W5 (rs379058) also displayed a significant association in the female schizophrenics (P = 0.016). Even after correction for multiple testing, these associations remained significant. Our findings suggest that the WDR3 gene may likely be a sensitive factor in female patients with schizophrenia, and that modification of the WDR3 signaling pathway warrants further investigation as to the pathophysiology of schizophrenia.
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Affiliation(s)
- Momoko Kobayashi
- Department of Psychiatry and Behavioral Sciences, Graduate School of Tokyo Medical and Dental University, Bunkyo-ku, Tokyo, Japan
| | - Daisuke Jitoku
- Department of Psychiatry and Behavioral Sciences, Graduate School of Tokyo Medical and Dental University, Bunkyo-ku, Tokyo, Japan
| | - Yoshimi Iwayama
- Laboratory for Molecular Psychiatry, RIKEN Brain Science Institute, Wako, Saitama, Japan
| | - Naoki Yamamoto
- Department of Psychiatry and Behavioral Sciences, Graduate School of Tokyo Medical and Dental University, Bunkyo-ku, Tokyo, Japan
| | - Tomoko Toyota
- Laboratory for Molecular Psychiatry, RIKEN Brain Science Institute, Wako, Saitama, Japan
| | - Katsuaki Suzuki
- Department of Psychiatry, Hamamatsu University School of Medicine, Hamamatsu, Shizuoka, Japan
| | - Mitsuru Kikuchi
- Department of Psychiatry and Neurobiology, Graduate School of Medical Science, Kanazawa University, Kanazawa, Ishikawa, Japan
| | - Tasuku Hashimoto
- Department of Psychiatry, Graduate School of Medicine, Chiba University, Chiba, Chiba, Japan
| | - Nobuhisa Kanahara
- Department of Psychiatry, Graduate School of Medicine, Chiba University, Chiba, Chiba, Japan
| | - Akeo Kurumaji
- Department of Psychiatry and Behavioral Sciences, Graduate School of Tokyo Medical and Dental University, Bunkyo-ku, Tokyo, Japan
| | - Takeo Yoshikawa
- Laboratory for Molecular Psychiatry, RIKEN Brain Science Institute, Wako, Saitama, Japan
| | - Toru Nishikawa
- Department of Psychiatry and Behavioral Sciences, Graduate School of Tokyo Medical and Dental University, Bunkyo-ku, Tokyo, Japan
- * E-mail:
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8
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Vincent NG, Charette JM, Baserga SJ. The SSU processome interactome in Saccharomyces cerevisiae reveals novel protein subcomplexes. RNA (NEW YORK, N.Y.) 2018; 24:77-89. [PMID: 29054886 PMCID: PMC5733573 DOI: 10.1261/rna.062927.117] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/11/2017] [Accepted: 10/03/2017] [Indexed: 05/05/2023]
Abstract
Ribosome assembly is an evolutionarily conserved and energy intensive process required for cellular growth, proliferation, and maintenance. In yeast, assembly of the small ribosomal subunit (SSU) requires approximately 75 assembly factors that act in coordination to form the SSU processome, a 6 MDa ribonucleoprotein complex. The SSU processome is required for processing, modifying, and folding the preribosomal RNA (rRNA) to prepare it for incorporation into the mature SSU. Although the protein composition of the SSU processome has been known for some time, the interaction network of the proteins required for its assembly has remained poorly defined. Here, we have used a semi-high-throughput yeast two-hybrid (Y2H) assay and coimmunoprecipitation validation method to produce a high-confidence interactome of SSU processome assembly factors (SPAFs), providing essential insight into SSU assembly and ribosome biogenesis. Further, we used glycerol density-gradient sedimentation to reveal the presence of protein subcomplexes that have not previously been observed. Our work not only provides essential insight into SSU assembly and ribosome biogenesis, but also serves as an important resource for future investigations into how defects in biogenesis and assembly cause congenital disorders of ribosomes known as ribosomopathies.
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Affiliation(s)
- Nicholas G Vincent
- Department of Microbiology, Yale University School of Medicine, New Haven, Connecticut 06520, USA
| | - J Michael Charette
- Department of Molecular Biophysics and Biochemistry, Yale University School of Medicine, New Haven, Connecticut 06520, USA
| | - Susan J Baserga
- Department of Molecular Biophysics and Biochemistry, Yale University School of Medicine, New Haven, Connecticut 06520, USA
- Department of Genetics, Yale University School of Medicine, New Haven, Connecticut, 06520, USA
- Department of Therapeutic Radiology, Yale University School of Medicine, New Haven, Connecticut 06520, USA
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9
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Hu J, Zhu X, Ye K. Structure and RNA recognition of ribosome assembly factor Utp30. RNA (NEW YORK, N.Y.) 2017; 23:1936-1945. [PMID: 28951391 PMCID: PMC5689012 DOI: 10.1261/rna.062695.117] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 06/26/2017] [Accepted: 09/21/2017] [Indexed: 06/07/2023]
Abstract
The 90S preribosomes are gigantic early assembly intermediates of small ribosomal subunits. Cryo-EM structures of 90S were recently determined, but many of its components have not been accurately modeled. Here we determine the crystal structure of yeast Utp30, a ribosomal L1 domain-containing protein in 90S, at 2.65 Å resolution, revealing a classic two-domain fold. The structure of Utp30 fits well into the cryo-EM density of 90S, confirming its previously assigned location. Utp30 binds to the rearranged helix 41 of 18S rRNA and helix 4 of 5' external transcribed spacer in 90S. Comparison of RNA-binding modes of different L1 domains illustrates that they consistently recognize a short RNA duplex with the concaved surface of domain I, but are versatile in RNA recognition outside the core interface. Cic1 is a paralog of Utp30 associating with large subunit preribosomes. Utp30 and Cic1 share similar RNA-binding modes, suggesting that their distinct functions may be executed by a single protein in other organisms. Deletion of Utp30 does not affect the composition of 90S. The nonessential role of Utp30 could be ascribed to its peripheral localization and redundant interactions in 90S.
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Affiliation(s)
- Jianfei Hu
- Key Laboratory of RNA Biology, CAS Center for Excellence in Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing 100101, China
- Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai 201203, China
- School of Life Science and Technology, ShanghaiTech University, Shanghai 201210, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Xing Zhu
- Key Laboratory of RNA Biology, CAS Center for Excellence in Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing 100101, China
| | - Keqiong Ye
- Key Laboratory of RNA Biology, CAS Center for Excellence in Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing 100101, China
- University of Chinese Academy of Sciences, Beijing 100049, China
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10
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Wang B, Ye K. Nop9 binds the central pseudoknot region of 18S rRNA. Nucleic Acids Res 2017; 45:3559-3567. [PMID: 28053123 PMCID: PMC5389560 DOI: 10.1093/nar/gkw1323] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/05/2016] [Accepted: 12/19/2016] [Indexed: 01/21/2023] Open
Abstract
The assembly of eukaryotic ribosomes requires numerous factors that transiently associate with evolving pre-ribosomal particles. The Pumilio repeat-containing protein Nop9 briefly associates with the 90S pre-ribosome during its co-transcriptional assembly. Here, we show that Nop9 specifically binds an 11-nucleotide sequence of 18S rRNA that forms the 3΄ side of the central pseudoknot and helix 28 in the mature subunit. Crystal structures of Nop9 in the free and RNA-bound states reveal a new type of Pumilio repeat protein with a distinct structure, target sequence and RNA-binding mode. Nop9 contains 10 Pumilio repeats arranged into a U-shaped scaffold. The target RNA is recognized by two stretches of repeats in a bipartite manner, and three central bases are unrecognized as a result of the degeneracy of repeats 6 and 7. Our data suggest that Nop9 regulates the folding of 18S rRNA at early assembly stages of 90S.
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Affiliation(s)
- Bing Wang
- Department of Biochemistry and Molecular Biology, College of Life Sciences, Beijing Normal University, Beijing 100875, China.,National Institute of Biological Sciences, Beijing 102206, China.,Key Laboratory of RNA Biology, CAS Center for Excellence in Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing 100101, China
| | - Keqiong Ye
- Key Laboratory of RNA Biology, CAS Center for Excellence in Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing 100101, China.,University of Chinese Academy of Sciences, Beijing 100049, China
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11
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Kressler D, Hurt E, Baßler J. A Puzzle of Life: Crafting Ribosomal Subunits. Trends Biochem Sci 2017; 42:640-654. [DOI: 10.1016/j.tibs.2017.05.005] [Citation(s) in RCA: 95] [Impact Index Per Article: 13.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2017] [Revised: 03/16/2017] [Accepted: 05/05/2017] [Indexed: 01/24/2023]
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12
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Boissier F, Schmidt CM, Linnemann J, Fribourg S, Perez-Fernandez J. Pwp2 mediates UTP-B assembly via two structurally independent domains. Sci Rep 2017; 7:3169. [PMID: 28600509 PMCID: PMC5466602 DOI: 10.1038/s41598-017-03034-y] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/03/2017] [Accepted: 04/21/2017] [Indexed: 11/24/2022] Open
Abstract
The SSU processome constitutes a large ribonucleoprotein complex involved in the early steps of ribosome biogenesis. UTP-B is one of the first multi-subunit protein complexes that associates with the pre-ribosomal RNA to form the SSU processome. To understand the molecular basis of the hierarchical assembly of the SSU-processome, we have undergone a structural and functional analysis of the UTP-B subunit Pwp2p. We show that Pwp2p is required for the proper assembly of UTP-B and for a productive association of UTP-B with pre-rRNA. These two functions are mediated by two distinct structural domains. The N-terminal domain of Pwp2p folds into a tandem WD-repeat (tWD) that associates with Utp21p, Utp18p, and Utp6p to form a core complex. The CTDs of Pwp2p and Utp21p mediate the assembly of the heterodimer Utp12p:Utp13p that is required for the stable incorporation of the UTP-B complex in the SSU processome. Finally, we provide evidence suggesting a role of UTP-B as a platform for the binding of assembly factors during the maturation of 20S rRNA precursors.
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Affiliation(s)
- Fanny Boissier
- Université de Bordeaux, INSERM U1212, CNRS 5320, Bordeaux, France
| | - Christina Maria Schmidt
- Universität Regensburg, Biochemie-Zentrum Regensburg (BZR), Lehrstuhl Biochemie III, D-93053, Regensburg, Germany
| | - Jan Linnemann
- Universität Regensburg, Biochemie-Zentrum Regensburg (BZR), Lehrstuhl Biochemie III, D-93053, Regensburg, Germany
| | | | - Jorge Perez-Fernandez
- Universität Regensburg, Biochemie-Zentrum Regensburg (BZR), Lehrstuhl Biochemie III, D-93053, Regensburg, Germany.
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13
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Sun Q, Zhu X, Qi J, An W, Lan P, Tan D, Chen R, Wang B, Zheng S, Zhang C, Chen X, Zhang W, Chen J, Dong MQ, Ye K. Molecular architecture of the 90S small subunit pre-ribosome. eLife 2017; 6. [PMID: 28244370 PMCID: PMC5354517 DOI: 10.7554/elife.22086] [Citation(s) in RCA: 104] [Impact Index Per Article: 14.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/07/2016] [Accepted: 02/26/2017] [Indexed: 12/12/2022] Open
Abstract
Eukaryotic small ribosomal subunits are first assembled into 90S pre-ribosomes. The complete 90S is a gigantic complex with a molecular mass of approximately five megadaltons. Here, we report the nearly complete architecture of Saccharomyces cerevisiae 90S determined from three cryo-electron microscopy single particle reconstructions at 4.5 to 8.7 angstrom resolution. The majority of the density maps were modeled and assigned to specific RNA and protein components. The nascent ribosome is assembled into isolated native-like substructures that are stabilized by abundant assembly factors. The 5' external transcribed spacer and U3 snoRNA nucleate a large subcomplex that scaffolds the nascent ribosome. U3 binds four sites of pre-rRNA, including a novel site on helix 27 but not the 3' side of the central pseudoknot, and crucially organizes the 90S structure. The 90S model provides significant insight into the principle of small subunit assembly and the function of assembly factors. DOI:http://dx.doi.org/10.7554/eLife.22086.001
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Affiliation(s)
- Qi Sun
- PTN Joint Graduate Program, School of Life Sciences, Tsinghua University, Beijing, China.,Key Laboratory of RNA Biology, Institute of Biophysics, CAS Center for Excellence in Biomacromolecules, Chinese Academy of Sciences, Beijing, China.,National Institute of Biological Sciences, Beijing, China
| | - Xing Zhu
- Key Laboratory of RNA Biology, Institute of Biophysics, CAS Center for Excellence in Biomacromolecules, Chinese Academy of Sciences, Beijing, China
| | - Jia Qi
- Key Laboratory of RNA Biology, Institute of Biophysics, CAS Center for Excellence in Biomacromolecules, Chinese Academy of Sciences, Beijing, China.,National Institute of Biological Sciences, Beijing, China.,Department of Biochemistry and Molecular Biology, College of Life Sciences, Beijing Normal University, Beijing, China
| | - Weidong An
- Key Laboratory of RNA Biology, Institute of Biophysics, CAS Center for Excellence in Biomacromolecules, Chinese Academy of Sciences, Beijing, China.,National Institute of Biological Sciences, Beijing, China.,College of Biological Sciences, China Agricultural University, Beijing, China
| | - Pengfei Lan
- National Institute of Biological Sciences, Beijing, China
| | - Dan Tan
- National Institute of Biological Sciences, Beijing, China
| | - Rongchang Chen
- Key Laboratory of RNA Biology, Institute of Biophysics, CAS Center for Excellence in Biomacromolecules, Chinese Academy of Sciences, Beijing, China
| | - Bing Wang
- Key Laboratory of RNA Biology, Institute of Biophysics, CAS Center for Excellence in Biomacromolecules, Chinese Academy of Sciences, Beijing, China.,National Institute of Biological Sciences, Beijing, China
| | - Sanduo Zheng
- National Institute of Biological Sciences, Beijing, China
| | - Cheng Zhang
- National Institute of Biological Sciences, Beijing, China
| | - Xining Chen
- National Institute of Biological Sciences, Beijing, China
| | - Wei Zhang
- National Institute of Biological Sciences, Beijing, China
| | - Jing Chen
- PTN Joint Graduate Program, School of Life Sciences, Tsinghua University, Beijing, China.,Key Laboratory of RNA Biology, Institute of Biophysics, CAS Center for Excellence in Biomacromolecules, Chinese Academy of Sciences, Beijing, China.,National Institute of Biological Sciences, Beijing, China
| | - Meng-Qiu Dong
- National Institute of Biological Sciences, Beijing, China
| | - Keqiong Ye
- Key Laboratory of RNA Biology, Institute of Biophysics, CAS Center for Excellence in Biomacromolecules, Chinese Academy of Sciences, Beijing, China.,University of Chinese Academy of Sciences, Beijing, China
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14
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Architecture of the 90S Pre-ribosome: A Structural View on the Birth of the Eukaryotic Ribosome. Cell 2017; 166:380-393. [PMID: 27419870 DOI: 10.1016/j.cell.2016.06.014] [Citation(s) in RCA: 158] [Impact Index Per Article: 22.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/26/2016] [Revised: 04/05/2016] [Accepted: 06/01/2016] [Indexed: 12/13/2022]
Abstract
The 90S pre-ribosome is an early biogenesis intermediate formed during co-transcriptional ribosome formation, composed of ∼70 assembly factors and several small nucleolar RNAs (snoRNAs) that associate with nascent pre-rRNA. We report the cryo-EM structure of the Chaetomium thermophilum 90S pre-ribosome, revealing how a network of biogenesis factors including 19 β-propellers and large α-solenoid proteins engulfs the pre-rRNA. Within the 90S pre-ribosome, we identify the UTP-A, UTP-B, Mpp10-Imp3-Imp4, Bms1-Rcl1, and U3 snoRNP modules, which are organized around 5'-ETS and partially folded 18S rRNA. The U3 snoRNP is strategically positioned at the center of the 90S particle to perform its multiple tasks during pre-rRNA folding and processing. The architecture of the elusive 90S pre-ribosome gives unprecedented structural insight into the early steps of pre-rRNA maturation. Nascent rRNA that is co-transcriptionally folded and given a particular shape by encapsulation within a dedicated mold-like structure is reminiscent of how polypeptides use chaperone chambers for their protein folding.
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15
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Chaker-Margot M, Barandun J, Hunziker M, Klinge S. Architecture of the yeast small subunit processome. Science 2016; 355:science.aal1880. [PMID: 27980088 DOI: 10.1126/science.aal1880] [Citation(s) in RCA: 98] [Impact Index Per Article: 12.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/12/2016] [Accepted: 12/05/2016] [Indexed: 12/21/2022]
Abstract
The small subunit (SSU) processome, a large ribonucleoprotein particle, organizes the assembly of the eukaryotic small ribosomal subunit by coordinating the folding, cleavage, and modification of nascent pre-ribosomal RNA (rRNA). Here, we present the cryo-electron microscopy structure of the yeast SSU processome at 5.1-angstrom resolution. The structure reveals how large ribosome biogenesis complexes assist the 5' external transcribed spacer and U3 small nucleolar RNA in providing an intertwined RNA-protein assembly platform for the separate maturation of 18S rRNA domains. The strategic placement of a molecular motor at the center of the particle further suggests a mechanism for mediating conformational changes within this giant particle. This study provides a structural framework for a mechanistic understanding of eukaryotic ribosome assembly in the model organism Saccharomyces cerevisiae.
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Affiliation(s)
- Malik Chaker-Margot
- Laboratory of Protein and Nucleic Acid Chemistry, The Rockefeller University, New York, NY 10065, USA.,Tri-Institutional Training Program in Chemical Biology, The Rockefeller University, New York, NY 10065, USA
| | - Jonas Barandun
- Laboratory of Protein and Nucleic Acid Chemistry, The Rockefeller University, New York, NY 10065, USA
| | - Mirjam Hunziker
- Laboratory of Protein and Nucleic Acid Chemistry, The Rockefeller University, New York, NY 10065, USA
| | - Sebastian Klinge
- Laboratory of Protein and Nucleic Acid Chemistry, The Rockefeller University, New York, NY 10065, USA.
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16
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Hunziker M, Barandun J, Petfalski E, Tan D, Delan-Forino C, Molloy KR, Kim KH, Dunn-Davies H, Shi Y, Chaker-Margot M, Chait BT, Walz T, Tollervey D, Klinge S. UtpA and UtpB chaperone nascent pre-ribosomal RNA and U3 snoRNA to initiate eukaryotic ribosome assembly. Nat Commun 2016; 7:12090. [PMID: 27354316 PMCID: PMC4931317 DOI: 10.1038/ncomms12090] [Citation(s) in RCA: 52] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/06/2016] [Accepted: 05/27/2016] [Indexed: 01/14/2023] Open
Abstract
Early eukaryotic ribosome biogenesis involves large multi-protein complexes, which co-transcriptionally associate with pre-ribosomal RNA to form the small subunit processome. The precise mechanisms by which two of the largest multi-protein complexes—UtpA and UtpB—interact with nascent pre-ribosomal RNA are poorly understood. Here, we combined biochemical and structural biology approaches with ensembles of RNA–protein cross-linking data to elucidate the essential functions of both complexes. We show that UtpA contains a large composite RNA-binding site and captures the 5′ end of pre-ribosomal RNA. UtpB forms an extended structure that binds early pre-ribosomal intermediates in close proximity to architectural sites such as an RNA duplex formed by the 5′ ETS and U3 snoRNA as well as the 3′ boundary of the 18S rRNA. Both complexes therefore act as vital RNA chaperones to initiate eukaryotic ribosome assembly. Eukaryotic ribosome biogenesis involves a large number of maturations factors which are responsible for the stepwise assembly of the ribosomal subunits. Here the authors use an array of biochemical and structural biology methods to investigate the function of the UtpA and UtpB complexes as part of the small subunit processome.
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Affiliation(s)
- Mirjam Hunziker
- Laboratory of Protein and Nucleic Acid Chemistry, The Rockefeller University, New York, New York 10065, USA
| | - Jonas Barandun
- Laboratory of Protein and Nucleic Acid Chemistry, The Rockefeller University, New York, New York 10065, USA
| | - Elisabeth Petfalski
- Wellcome Trust Centre for Cell Biology, University of Edinburgh, Michael Swann Building, Max Born Crescent, Edinburgh EH9 3BF, UK
| | - Dongyan Tan
- Department of Cell Biology, Harvard Medical School, Boston, Massachusetts 02115, USA
| | - Clémentine Delan-Forino
- Wellcome Trust Centre for Cell Biology, University of Edinburgh, Michael Swann Building, Max Born Crescent, Edinburgh EH9 3BF, UK
| | - Kelly R Molloy
- Laboratory of Mass Spectrometry and Gaseous Ion Chemistry, The Rockefeller University, New York, New York 10065, USA
| | - Kelly H Kim
- Laboratory of Molecular Electron Microscopy, The Rockefeller University, New York, New York 10065, USA
| | - Hywel Dunn-Davies
- Wellcome Trust Centre for Cell Biology, University of Edinburgh, Michael Swann Building, Max Born Crescent, Edinburgh EH9 3BF, UK
| | - Yi Shi
- Laboratory of Mass Spectrometry and Gaseous Ion Chemistry, The Rockefeller University, New York, New York 10065, USA
| | - Malik Chaker-Margot
- Laboratory of Protein and Nucleic Acid Chemistry, The Rockefeller University, New York, New York 10065, USA.,Tri-Institutional Training Program in Chemical Biology, The Rockefeller University, New York, New York 10065, USA
| | - Brian T Chait
- Laboratory of Mass Spectrometry and Gaseous Ion Chemistry, The Rockefeller University, New York, New York 10065, USA
| | - Thomas Walz
- Laboratory of Molecular Electron Microscopy, The Rockefeller University, New York, New York 10065, USA
| | - David Tollervey
- Wellcome Trust Centre for Cell Biology, University of Edinburgh, Michael Swann Building, Max Born Crescent, Edinburgh EH9 3BF, UK
| | - Sebastian Klinge
- Laboratory of Protein and Nucleic Acid Chemistry, The Rockefeller University, New York, New York 10065, USA
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17
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Zhang C, Sun Q, Chen R, Chen X, Lin J, Ye K. Integrative structural analysis of the UTPB complex, an early assembly factor for eukaryotic small ribosomal subunits. Nucleic Acids Res 2016; 44:7475-86. [PMID: 27330138 PMCID: PMC5009746 DOI: 10.1093/nar/gkw562] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/12/2016] [Accepted: 06/10/2016] [Indexed: 12/28/2022] Open
Abstract
Ribosome assembly is an essential and conserved cellular process in eukaryotes that requires numerous assembly factors. The six-subunit UTPB complex is an essential component of the 90S precursor of the small ribosomal subunit. Here, we analyzed the molecular architecture of UTPB using an integrative structural biology approach. We mapped the major interactions that associate each of six UTPB proteins. Crystallographic studies showed that Utp1, Utp21, Utp12 and Utp13 are evolutionarily related and form a dimer of dimers (Utp1–Utp21, Utp12–Utp13) through their homologous helical C-terminal domains. Molecular docking with crosslinking restraints showed that the WD domains of Utp12 and Utp13 are associated, as are the WD domains of Utp1, Utp21 and Utp18. Electron microscopy images of the entire UTPB complex revealed that it predominantly adopts elongated conformations and possesses internal flexibility. We also determined crystal structures of the WD domain of Utp18 and the HAT and deviant HAT domains of Utp6. A structural model of UTPB was derived based on these data.
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Affiliation(s)
- Cheng Zhang
- National Institute of Biological Sciences, Beijing 102206, China
| | - Qi Sun
- National Institute of Biological Sciences, Beijing 102206, China Peking University-Tsinghua University-National Institute of Biological Sciences Joint Graduate Program, School of Life Sciences, Tsinghua University, Beijing 100084, China Key Laboratory of RNA Biology, CAS Center for Excellence in Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing 100101, China Beijing Key Laboratory of Noncoding RNA, CAS Center for Excellence in Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing 100101, China
| | - Rongchang Chen
- Key Laboratory of RNA Biology, CAS Center for Excellence in Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing 100101, China Beijing Key Laboratory of Noncoding RNA, CAS Center for Excellence in Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing 100101, China
| | - Xining Chen
- National Institute of Biological Sciences, Beijing 102206, China
| | - Jinzhong Lin
- National Institute of Biological Sciences, Beijing 102206, China
| | - Keqiong Ye
- Key Laboratory of RNA Biology, CAS Center for Excellence in Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing 100101, China Beijing Key Laboratory of Noncoding RNA, CAS Center for Excellence in Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing 100101, China
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18
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Pöll G, Li S, Ohmayer U, Hierlmeier T, Milkereit P, Perez-Fernandez J. In vitro reconstitution of yeast tUTP/UTP A and UTP B subcomplexes provides new insights into their modular architecture. PLoS One 2014; 9:e114898. [PMID: 25501974 PMCID: PMC4264851 DOI: 10.1371/journal.pone.0114898] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2014] [Accepted: 11/14/2014] [Indexed: 11/29/2022] Open
Abstract
Eukaryotic ribosome biogenesis is a multistep process involving more than 150 biogenesis factors, which interact transiently with pre-ribosomal particles to promote their maturation. Some of these auxiliary proteins have been isolated in complexes found separate from the ribosomal environment. Among them, are 3 large UTP subcomplexes containing 6 or 7 protein subunits which are involved in the early steps of ribosome biogenesis. The composition of the UTP subcomplexes and the network of binary interactions between protein subunits have been analyzed previously. To obtain further insights into the structural and biochemical properties of UTP subcomplexes, we established a heterologous expression system to allow reconstitution of the yeast tUTP/UTP A and UTP B subcomplexes from their candidate subunits. The results of a series of reconstitution experiments involving different combinations of protein subunits are in good agreement with most of the previously observed binary interactions. Moreover, in combination with additional biochemical analyses, several stable building blocks of the UTP subcomplexes were identified. Based on these findings, we present a refined model of the tUTP/UTP A and UTP B architecture.
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Affiliation(s)
- Gisela Pöll
- Lehrstuhl für Biochemie III, Universität Regensburg, Regensburg, Germany
| | - Shuang Li
- Lehrstuhl für Biochemie III, Universität Regensburg, Regensburg, Germany
| | - Uli Ohmayer
- Lehrstuhl für Biochemie III, Universität Regensburg, Regensburg, Germany
| | - Thomas Hierlmeier
- Lehrstuhl für Biochemie III, Universität Regensburg, Regensburg, Germany
| | - Philipp Milkereit
- Lehrstuhl für Biochemie III, Universität Regensburg, Regensburg, Germany
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19
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Zheng S, Lan P, Liu X, Ye K. Interaction between ribosome assembly factors Krr1 and Faf1 is essential for formation of small ribosomal subunit in yeast. J Biol Chem 2014; 289:22692-22703. [PMID: 24990943 DOI: 10.1074/jbc.m114.584490] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022] Open
Abstract
Ribosome formation in Saccharomyces cerevisiae requires a large number of transiently associated assembly factors that coordinate processing and folding of pre-rRNA and binding of ribosomal proteins. Krr1 and Faf1 are two interacting proteins present in early 90 S precursor particles of the small ribosomal subunit. Here, we determined a co-crystal structure of the core domain of Krr1 bound to a 19-residue fragment of Faf1 at 2.8 Å resolution. The structure reveals that Krr1 consists of two packed K homology (KH) domains, KH1 and KH2, and resembles archaeal Dim2-like proteins. We show that KH1 is a divergent KH domain that lacks the RNA-binding GXXG motif and is involved in binding another assembly factor, Kri1. KH2 contains a canonical RNA-binding surface and additionally associates with an α-helix of Faf1. Specific disruption of the Krr1-Faf1 interaction impaired early 18 S rRNA processing at sites A0, A1, and A2 and caused cell lethality, but it did not prevent incorporation of the two proteins into pre-ribosomes. The Krr1-Faf1 interaction likely maintains a critical conformation of 90 S pre-ribosomes required for pre-rRNA processing. Our results illustrate the versatility of KH domains in protein interaction and provide insight into the role of Krr1-Faf1 interaction in ribosome biogenesis.
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Affiliation(s)
- Sanduo Zheng
- Department of Biochemistry and Molecular Biology, College of Life Sciences, Beijing Normal University, Beijing 100875,; National Institute of Biological Sciences at Beijing, Beijing 102206, and
| | - Pengfei Lan
- National Institute of Biological Sciences at Beijing, Beijing 102206, and; Graduate School of Peking Union Medical College and Chinese Academy of Medical Sciences, Beijing 100730
| | - Ximing Liu
- National Institute of Biological Sciences at Beijing, Beijing 102206, and
| | - Keqiong Ye
- National Institute of Biological Sciences at Beijing, Beijing 102206, and; Graduate School of Peking Union Medical College and Chinese Academy of Medical Sciences, Beijing 100730,; Laboratory of RNA Biology, Institute of Biophysics, Chinese Academy of Sciences, Beijing 100101, China.
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