1
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In vitro characterization of Dhr1 from Saccharomyces cerevisiae. Methods Enzymol 2022; 673:77-101. [DOI: 10.1016/bs.mie.2022.03.058] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
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2
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Liu Y, Xu W, Xu X, Tan Z, Xu J, Ma L, Du P, Yang Y. Loss of BRMS2 induces cell growth inhibition and translation capacity reduction in colorectal cancer cells. Am J Cancer Res 2021; 11:930-944. [PMID: 33791164 PMCID: PMC7994161] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/09/2020] [Accepted: 01/12/2021] [Indexed: 06/12/2023] Open
Abstract
A variety of chemotherapeutic drugs targeting ribosome processing have been developed and applied to cancer treatment mainly based on the impaired ribosome biogenesis checkpoint (IRBC). The IMP U3 small nucleolar ribonucleoprotein 3 (IMP3, BRMS2) has been identified as a participant in pre-rRNA processing for nearly twenty years. However, the roles of BRMS2 in cancers still unknown. In this research, a tissue microarray (TMA) with 151 paired tissues showed the aberrant overexpression of BRMS2 in CRC tissues which was associated with the worse prognosis. To clarify the function of BRMS2 in CRC cells, an inducible knockdown system was introduced in vitro and in vivo and the cell growth was drastically suppressed. Mechanistically, we found depletion of BRMS2 markedly decreased the protein translation rates which can limit cell growth. Furthermore, to confirm whether the IRBC played a role, multiple approaches including detection of the p53 pathway, depletion of BRMS2 in p53-mutated SW620 cells, and co-depletion of RPL11 were taken. To our surprise, IRBC was not activated. That indicated BRMS2 may play a unique role in ribosome biosynthesis and IRBC. Taken together, our results demonstrated the oncogenic function of BRMS2 in CRC cells and supported its potential as a therapeutic target.
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Affiliation(s)
- Yaofu Liu
- Suzhou Institute of Systems Medicine, Chinese Academy of Medical Sciences & Peking Union Medical CollegeSuzhou, China
| | - Weimin Xu
- Department of Colorectal Surgery, Xin-Hua Hospital, Shanghai Jiaotong University School of MedicineShanghai, China
| | - Xin Xu
- Suzhou Institute of Systems Medicine, Chinese Academy of Medical Sciences & Peking Union Medical CollegeSuzhou, China
| | - Zhengzhi Tan
- Department of Computer Science, University of Alabama at BirminghamBirmingham, USA
| | - Jing Xu
- International School for Advanced Studies (SISSA)Trieste, Italy
| | - Lei Ma
- Suzhou Institute of Systems Medicine, Chinese Academy of Medical Sciences & Peking Union Medical CollegeSuzhou, China
| | - Peng Du
- Department of Colorectal Surgery, Xin-Hua Hospital, Shanghai Jiaotong University School of MedicineShanghai, China
| | - Yili Yang
- Suzhou Institute of Systems Medicine, Chinese Academy of Medical Sciences & Peking Union Medical CollegeSuzhou, China
- China Regional Research Center, International Centre for Genetic Engineering and BiotechnologyTaizhou, Jiangsu, China
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3
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Bud23 promotes the final disassembly of the small subunit Processome in Saccharomyces cerevisiae. PLoS Genet 2020; 16:e1009215. [PMID: 33306676 PMCID: PMC7758049 DOI: 10.1371/journal.pgen.1009215] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/02/2020] [Revised: 12/23/2020] [Accepted: 10/21/2020] [Indexed: 01/18/2023] Open
Abstract
The first metastable assembly intermediate of the eukaryotic ribosomal small subunit (SSU) is the SSU Processome, a large complex of RNA and protein factors that is thought to represent an early checkpoint in the assembly pathway. Transition of the SSU Processome towards continued maturation requires the removal of the U3 snoRNA and biogenesis factors as well as ribosomal RNA processing. While the factors that drive these events are largely known, how they do so is not. The methyltransferase Bud23 has a role during this transition, but its function, beyond the nonessential methylation of ribosomal RNA, is not characterized. Here, we have carried out a comprehensive genetic screen to understand Bud23 function. We identified 67 unique extragenic bud23Δ-suppressing mutations that mapped to genes encoding the SSU Processome factors DHR1, IMP4, UTP2 (NOP14), BMS1 and the SSU protein RPS28A. These factors form a physical interaction network that links the binding site of Bud23 to the U3 snoRNA and many of the amino acid substitutions weaken protein-protein and protein-RNA interactions. Importantly, this network links Bud23 to the essential GTPase Bms1, which acts late in the disassembly pathway, and the RNA helicase Dhr1, which catalyzes U3 snoRNA removal. Moreover, particles isolated from cells lacking Bud23 accumulated late SSU Processome factors and ribosomal RNA processing defects. We propose a model in which Bud23 dissociates factors surrounding its binding site to promote SSU Processome progression. Ribosomes are the molecular machines that synthesize proteins and are composed of a large and a small subunit which carry out the essential functions of polypeptide synthesis and mRNA decoding, respectively. Ribosome production is tightly linked to cellular growth as cells must produce enough ribosomes to meet their protein needs. However, ribosome assembly is a metabolically expensive pathway that must be balanced with other cellular energy needs and regulated accordingly. In eukaryotes, the small subunit (SSU) Processome is a metastable intermediate that ultimately progresses towards a mature SSU through the release of biogenesis factors. The decision to progress the SSU Processome is thought to be an early checkpoint in the SSU assembly pathway, but insight into the mechanisms of progression is needed. Previous studies suggest that Bud23 plays an uncharacterized role during SSU Processome progression. Here, we used a genetic approach to understand its function and found that Bud23 is connected to a network of SSU Processome factors that stabilize the particle. Interestingly, two of these factors are enzymes that are needed for progression. We conclude that Bud23 promotes the release of factors surrounding its binding site to induce structural rearrangements during the progression of the SSU Processome.
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Pokornowska M, Milewski MC, Ciechanowska K, Szczepańska A, Wojnicka M, Radogostowicz Z, Figlerowicz M, Kurzynska-Kokorniak A. The RNA-RNA base pairing potential of human Dicer and Ago2 proteins. Cell Mol Life Sci 2020; 77:3231-3244. [PMID: 31655860 PMCID: PMC7391396 DOI: 10.1007/s00018-019-03344-6] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/19/2019] [Revised: 09/24/2019] [Accepted: 10/14/2019] [Indexed: 12/22/2022]
Abstract
The ribonuclease Dicer produces microRNAs (miRNAs) and small interfering RNAs that are handed over to Ago proteins to control gene expression by targeting complementary sequences within transcripts. Interestingly, a growing number of reports have demonstrated that the activity of Dicer may extend beyond the biogenesis of small regulatory RNAs. Among them, a report from our latest studies revealed that human Dicer facilitates base pairing of complementary sequences present in two nucleic acids, thus acting as a nucleic acid annealer. Accordingly, in this manuscript, we address how RNA structure influences the annealing activity of human Dicer. We show that Dicer supports hybridization between a small RNA and a complementary sequence of a longer RNA in vitro, even when both complementary sequences are trapped within secondary structures. Moreover, we show that under applied conditions, human Ago2, a core component of RNA-induced silencing complex, displays very limited annealing activity. Based on the available data from new-generation sequencing experiments regarding the RNA pool bound to Dicer in vivo, we show that multiple Dicer-binding sites within mRNAs also contain miRNA targets. Subsequently, we demonstrate in vitro that Dicer but not Ago2 can anneal miRNA to its target present within mRNA. We hypothesize that not all miRNA duplexes are handed over to Ago proteins. Instead, miRNA-Dicer complexes could target specific sequences within transcripts and either compete or cooperate for binding sites with miRNA-Ago complexes. Thus, not only Ago but also Dicer might be directly involved in the posttranscriptional control of gene expression.
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Affiliation(s)
- Maria Pokornowska
- Department of Ribonucleoprotein Biochemistry, Institute of Bioorganic Chemistry, Polish Academy of Sciences, 61-704, Poznan, Poland
| | - Marek C Milewski
- Department of Molecular and Systems Biology, Institute of Bioorganic Chemistry, Polish Academy of Sciences, 61-704, Poznan, Poland
| | - Kinga Ciechanowska
- Department of Ribonucleoprotein Biochemistry, Institute of Bioorganic Chemistry, Polish Academy of Sciences, 61-704, Poznan, Poland
| | - Agnieszka Szczepańska
- Department of Ribonucleoprotein Biochemistry, Institute of Bioorganic Chemistry, Polish Academy of Sciences, 61-704, Poznan, Poland
| | - Marta Wojnicka
- Department of Ribonucleoprotein Biochemistry, Institute of Bioorganic Chemistry, Polish Academy of Sciences, 61-704, Poznan, Poland
| | - Ziemowit Radogostowicz
- Department of Ribonucleoprotein Biochemistry, Institute of Bioorganic Chemistry, Polish Academy of Sciences, 61-704, Poznan, Poland
| | - Marek Figlerowicz
- Department of Molecular and Systems Biology, Institute of Bioorganic Chemistry, Polish Academy of Sciences, 61-704, Poznan, Poland
- Institute of Computing Science, Poznan University of Technology, 60-965, Poznan, Poland
| | - Anna Kurzynska-Kokorniak
- Department of Ribonucleoprotein Biochemistry, Institute of Bioorganic Chemistry, Polish Academy of Sciences, 61-704, Poznan, Poland.
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5
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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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6
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Rothé B, Manival X, Rolland N, Charron C, Senty-Ségault V, Branlant C, Charpentier B. Implication of the box C/D snoRNP assembly factor Rsa1p in U3 snoRNP assembly. Nucleic Acids Res 2017; 45:7455-7473. [PMID: 28505348 PMCID: PMC5499572 DOI: 10.1093/nar/gkx424] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/08/2016] [Accepted: 05/02/2017] [Indexed: 01/23/2023] Open
Abstract
The U3 box C/D snoRNA is one key element of 90S pre-ribosome. It contains a 5΄ domain pairing with pre-rRNA and the U3B/C and U3C΄/D motifs for U3 packaging into a unique small nucleolar ribonucleoprotein particle (snoRNP). The RNA-binding protein Snu13/SNU13 nucleates on U3B/C the assembly of box C/D proteins Nop1p/FBL and Nop56p/NOP56, and the U3-specific protein Rrp9p/U3-55K. Snu13p/SNU13 has a much lower affinity for U3C΄/D but nevertheless forms on this motif an RNP with box C/D proteins Nop1p/FBL and Nop58p/NOP58. In this study, we characterized the influence of the RNP assembly protein Rsa1 in the early steps of U3 snoRNP biogenesis in yeast and we propose a refined model of U3 snoRNP biogenesis. While recombinant Snu13p enhances the binding of Rrp9p to U3B/C, we observed that Rsa1p has no effect on this activity but forms with Snu13p and Rrp9p a U3B/C pre-RNP. In contrast, we found that Rsa1p enhances Snu13p binding on U3C΄/D. RNA footprinting experiments indicate that this positive effect most likely occurs by direct contacts of Rsa1p with the U3 snoRNA 5΄ domain. In light of the recent U3 snoRNP cryo-EM structures, our data suggest that Rsa1p has a dual role by also preventing formation of a pre-mature functional U3 RNP.
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Affiliation(s)
- Benjamin Rothé
- Ingénierie Moléculaire et Physiopathologie Articulaire (IMoPA), UMR 7365 CNRS Université de Lorraine, Biopôle, Campus Biologie Santé, 9 avenue de la forêt de Haye, BP 20199, 54505 Vandœuvre-lès-Nancy, France
| | - Xavier Manival
- Ingénierie Moléculaire et Physiopathologie Articulaire (IMoPA), UMR 7365 CNRS Université de Lorraine, Biopôle, Campus Biologie Santé, 9 avenue de la forêt de Haye, BP 20199, 54505 Vandœuvre-lès-Nancy, France
| | - Nicolas Rolland
- Ingénierie Moléculaire et Physiopathologie Articulaire (IMoPA), UMR 7365 CNRS Université de Lorraine, Biopôle, Campus Biologie Santé, 9 avenue de la forêt de Haye, BP 20199, 54505 Vandœuvre-lès-Nancy, France
| | - Christophe Charron
- Ingénierie Moléculaire et Physiopathologie Articulaire (IMoPA), UMR 7365 CNRS Université de Lorraine, Biopôle, Campus Biologie Santé, 9 avenue de la forêt de Haye, BP 20199, 54505 Vandœuvre-lès-Nancy, France
| | - Véronique Senty-Ségault
- Ingénierie Moléculaire et Physiopathologie Articulaire (IMoPA), UMR 7365 CNRS Université de Lorraine, Biopôle, Campus Biologie Santé, 9 avenue de la forêt de Haye, BP 20199, 54505 Vandœuvre-lès-Nancy, France
| | - Christiane Branlant
- Ingénierie Moléculaire et Physiopathologie Articulaire (IMoPA), UMR 7365 CNRS Université de Lorraine, Biopôle, Campus Biologie Santé, 9 avenue de la forêt de Haye, BP 20199, 54505 Vandœuvre-lès-Nancy, France
| | - Bruno Charpentier
- Ingénierie Moléculaire et Physiopathologie Articulaire (IMoPA), UMR 7365 CNRS Université de Lorraine, Biopôle, Campus Biologie Santé, 9 avenue de la forêt de Haye, BP 20199, 54505 Vandœuvre-lès-Nancy, France
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7
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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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8
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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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9
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Tomecki R, Labno A, Drazkowska K, Cysewski D, Dziembowski A. hUTP24 is essential for processing of the human rRNA precursor at site A1, but not at site A0. RNA Biol 2016; 12:1010-29. [PMID: 26237581 DOI: 10.1080/15476286.2015.1073437] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/05/2023] Open
Abstract
Production of ribosomes relies on more than 200 accessory factors to ensure the proper sequence of steps and faultless assembly of ribonucleoprotein machinery. Among trans-acting factors are numerous enzymes, including ribonucleases responsible for processing the large rRNA precursor synthesized by RNA polymerase I that encompasses sequences corresponding to mature 18S, 5.8S, and 25/28S rRNA. In humans, the identity of most enzymes responsible for individual processing steps, including endoribonucleases that cleave pre-rRNA at specific sites within regions flanking and separating mature rRNA, remains largely unknown. Here, we investigated the role of hUTP24 in rRNA maturation in human cells. hUTP24 is a human homolog of the Saccharomyces cerevisiae putative PIN domain-containing endoribonuclease Utp24 (yUtp24), which was suggested to participate in the U3 snoRNA-dependent processing of yeast pre-rRNA at sites A0, A1, and A2. We demonstrate that hUTP24 interacts to some extent with proteins homologous to the components of the yeast small subunit (SSU) processome. Moreover, mutation in the putative catalytic site of hUTP24 results in slowed growth of cells and reduced metabolic activity. These effects are associated with a defect in biogenesis of the 40S ribosomal subunit, which results from decreased amounts of 18S rRNA as a consequence of inaccurate pre-rRNA processing at the 5'-end of the 18S rRNA segment (site A1). Interestingly, and in contrast to yeast, site A0 located upstream of A1 is efficiently processed upon UTP24 dysfunction. Finally, hUTP24 inactivation leads to aberrant processing of 18S rRNA 2 nucleotides downstream of the normal A1 cleavage site.
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Affiliation(s)
- Rafal Tomecki
- a Institute of Biochemistry and Biophysics; Polish Academy of Sciences ; Warsaw , Poland.,b Institute of Genetics and Biotechnology; Faculty of Biology; University of Warsaw ; Warsaw , Poland
| | - Anna Labno
- a Institute of Biochemistry and Biophysics; Polish Academy of Sciences ; Warsaw , Poland.,b Institute of Genetics and Biotechnology; Faculty of Biology; University of Warsaw ; Warsaw , Poland
| | - Karolina Drazkowska
- a Institute of Biochemistry and Biophysics; Polish Academy of Sciences ; Warsaw , Poland.,b Institute of Genetics and Biotechnology; Faculty of Biology; University of Warsaw ; Warsaw , Poland
| | - Dominik Cysewski
- a Institute of Biochemistry and Biophysics; Polish Academy of Sciences ; Warsaw , Poland.,b Institute of Genetics and Biotechnology; Faculty of Biology; University of Warsaw ; Warsaw , Poland
| | - Andrzej Dziembowski
- a Institute of Biochemistry and Biophysics; Polish Academy of Sciences ; Warsaw , Poland.,b Institute of Genetics and Biotechnology; Faculty of Biology; University of Warsaw ; Warsaw , Poland
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10
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Utp14 Recruits and Activates the RNA Helicase Dhr1 To Undock U3 snoRNA from the Preribosome. Mol Cell Biol 2016; 36:965-78. [PMID: 26729466 DOI: 10.1128/mcb.00773-15] [Citation(s) in RCA: 47] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/07/2015] [Accepted: 12/28/2015] [Indexed: 01/24/2023] Open
Abstract
In eukaryotic ribosome biogenesis, U3 snoRNA base pairs with the pre-rRNA to promote its processing. However, U3 must be removed to allow folding of the central pseudoknot, a key feature of the small subunit. Previously, we showed that the DEAH/RHA RNA helicase Dhr1 dislodges U3 from the pre-rRNA. DHR1 can be linked to UTP14, encoding an essential protein of the preribosome, through genetic interactions with the rRNA methyltransferase Bud23. Here, we report that Utp14 regulates Dhr1. Mutations within a discrete region of Utp14 reduced interaction with Dhr1 that correlated with reduced function of Utp14. These mutants accumulated Dhr1 and U3 in a pre-40S particle, mimicking a helicase-inactive Dhr1 mutant. This similarity in the phenotypes led us to propose that Utp14 activates Dhr1. Indeed, Utp14 formed a complex with Dhr1 and stimulated its unwinding activity in vitro. Moreover, the utp14 mutants that mimicked a catalytically inactive dhr1 mutant in vivo showed reduced stimulation of unwinding activity in vitro. Dhr1 binding to the preribosome was substantially reduced only when both Utp14 and Bud23 were depleted. Thus, Utp14 is bifunctional; together with Bud23, it is needed for stable interaction of Dhr1 with the preribosome, and Utp14 activates Dhr1 to dislodge U3.
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11
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Abstract
In this study, Madru et al. determined the structure of the ribosome-bound Rpf2–Rrs1 complex, a complex essential for the assembly of the 5S RNA in ribosomes, and characterized the free and 5S-bound structures. The findings show that Rpf2 and Rrs1 establish a network of protein–protein and protein–RNA interactions with the 5S RNA and specific preribosomes, thus providing novel insight into ribosome biogenesis. In eukaryotes, three of the four ribosomal RNAs (rRNAs)—the 5.8S, 18S, and 25S/28S rRNAs—are processed from a single pre-rRNA transcript and assembled into ribosomes. The fourth rRNA, the 5S rRNA, is transcribed by RNA polymerase III and is assembled into the 5S ribonucleoprotein particle (RNP), containing ribosomal proteins Rpl5/uL18 and Rpl11/uL5, prior to its incorporation into preribosomes. In mammals, the 5S RNP is also a central regulator of the homeostasis of the tumor suppressor p53. The nucleolar localization of the 5S RNP and its assembly into preribosomes are performed by a specialized complex composed of Rpf2 and Rrs1 in yeast or Bxdc1 and hRrs1 in humans. Here we report the structural and functional characterization of the Rpf2–Rrs1 complex alone, in complex with the 5S RNA, and within pre-60S ribosomes. We show that the Rpf2–Rrs1 complex contains a specialized 5S RNA E-loop-binding module, contacts the Rpl5 protein, and also contacts the ribosome assembly factor Rsa4 and the 25S RNA. We propose that the Rpf2–Rrs1 complex establishes a network of interactions that guide the incorporation of the 5S RNP in preribosomes in the initial conformation prior to its rotation to form the central protuberance found in the mature large ribosomal subunit.
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12
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Asano N, Kato K, Nakamura A, Komoda K, Tanaka I, Yao M. Structural and functional analysis of the Rpf2-Rrs1 complex in ribosome biogenesis. Nucleic Acids Res 2015; 43:4746-57. [PMID: 25855814 PMCID: PMC4482071 DOI: 10.1093/nar/gkv305] [Citation(s) in RCA: 36] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/03/2015] [Accepted: 03/27/2015] [Indexed: 11/28/2022] Open
Abstract
Proteins Rpf2 and Rrs1 are required for 60S ribosomal subunit maturation. These proteins are necessary for the recruitment of three ribosomal components (5S ribosomal RNA [rRNA], RpL5 and RpL11) to the 90S ribosome precursor and subsequent 27SB pre-rRNA processing. Here we present the crystal structure of the Aspergillus nidulans (An) Rpf2-Rrs1 core complex. The core complex contains the tightly interlocked N-terminal domains of Rpf2 and Rrs1. The Rpf2 N-terminal domain includes a Brix domain characterized by similar N- and C-terminal architecture. The long α-helix of Rrs1 joins the C-terminal half of the Brix domain as if it were part of a single molecule. The conserved proline-rich linker connecting the N- and C-terminal domains of Rrs1 wrap around the side of Rpf2 and anchor the C-terminal domain of Rrs1 to a specific site on Rpf2. In addition, gel shift analysis revealed that the Rpf2-Rrs1 complex binds directly to 5S rRNA. Further analysis of Rpf2-Rrs1 mutants demonstrated that Saccharomyces cerevisiae Rpf2 R236 (corresponds to R238 of AnRpf2) plays a significant role in this binding. Based on these studies and previous reports, we have proposed a model for ribosomal component recruitment to the 90S ribosome precursor.
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Affiliation(s)
- Nozomi Asano
- Graduate School of Life Science, Hokkaido University, Sapporo 060-0810, Japan
| | - Koji Kato
- Graduate School of Life Science, Hokkaido University, Sapporo 060-0810, Japan Faculty of Advanced Life Science, Hokkaido University, Sapporo 060-0810, Japan
| | - Akiyoshi Nakamura
- Faculty of Advanced Life Science, Hokkaido University, Sapporo 060-0810, Japan
| | - Keisuke Komoda
- Graduate School of Life Science, Hokkaido University, Sapporo 060-0810, Japan Faculty of Advanced Life Science, Hokkaido University, Sapporo 060-0810, Japan
| | - Isao Tanaka
- Faculty of Advanced Life Science, Hokkaido University, Sapporo 060-0810, Japan
| | - Min Yao
- Graduate School of Life Science, Hokkaido University, Sapporo 060-0810, Japan Faculty of Advanced Life Science, Hokkaido University, Sapporo 060-0810, Japan
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13
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The DEAH-box helicase Dhr1 dissociates U3 from the pre-rRNA to promote formation of the central pseudoknot. PLoS Biol 2015; 13:e1002083. [PMID: 25710520 PMCID: PMC4340053 DOI: 10.1371/journal.pbio.1002083] [Citation(s) in RCA: 60] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2014] [Accepted: 01/16/2015] [Indexed: 11/19/2022] Open
Abstract
In eukaryotes, the highly conserved U3 small nucleolar RNA (snoRNA) base-pairs to multiple sites in the pre-ribosomal RNA (pre-rRNA) to promote early cleavage and folding events. Binding of the U3 box A region to the pre-rRNA is mutually exclusive with folding of the central pseudoknot (CPK), a universally conserved rRNA structure of the small ribosomal subunit essential for protein synthesis. Here, we report that the DEAH-box helicase Dhr1 (Ecm16) is responsible for displacing U3. An active site mutant of Dhr1 blocked release of U3 from the pre-ribosome, thereby trapping a pre-40S particle. This particle had not yet achieved its mature structure because it contained U3, pre-rRNA, and a number of early-acting ribosome synthesis factors but noticeably lacked ribosomal proteins (r-proteins) that surround the CPK. Dhr1 was cross-linked in vivo to the pre-rRNA and to U3 sequences flanking regions that base-pair to the pre-rRNA including those that form the CPK. Point mutations in the box A region of U3 suppressed a cold-sensitive mutation of Dhr1, strongly indicating that U3 is an in vivo substrate of Dhr1. To support the conclusions derived from in vivo analysis we showed that Dhr1 unwinds U3-18S duplexes in vitro by using a mechanism reminiscent of DEAD box proteins. U3 snoRNA binds to pre-rRNA, helping to orchestrate key steps in ribosome assembly. This study identifies Dhr1 as the essential RNA helicase that releases U3 snoRNA and allows ribosome maturation to continue. Ribosomes are intricate assemblies of RNA and protein that are responsible for decoding a cell’s genetic information. Their assembly is a very rapid and dynamic process, requiring many ancillary factors in eukaryotic cells. One critical factor is the U3 snoRNA, which binds to the immature ribosomal RNA to direct early processing and folding of the RNA of the small subunit. Although U3 is essential to promote assembly, it must be actively removed to allow completion of RNA folding. Such RNA dynamics are often driven by RNA helicases, and here we use a broad range of experimental approaches to identify the RNA helicase Dhr1 as the enzyme responsible for removing U3 in yeast. A combination of techniques allows us to assess what goes wrong when Dhr1 is mutated, which parts of the RNA molecules the enzyme binds to, and how Dhr1 unwinds its substrates.
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14
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Feng JM, Tian HF, Wen JF. Origin and evolution of the eukaryotic SSU processome revealed by a comprehensive genomic analysis and implications for the origin of the nucleolus. Genome Biol Evol 2014; 5:2255-67. [PMID: 24214024 PMCID: PMC3879963 DOI: 10.1093/gbe/evt173] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022] Open
Abstract
As a nucleolar complex for small-subunit (SSU) ribosomal RNA processing, SSU processome
has been extensively studied mainly in Saccharomyces cerevisiae but not
in diverse organisms, leaving open the question of whether it is a ubiquitous mechanism
across eukaryotes and how it evolved in the course of the evolution of eukaryotes.
Genome-wide survey and identification of SSU processome components showed that the
majority of all 77 yeast SSU processome proteins possess homologs in almost all of the
main eukaryotic lineages, and 14 of them have homologs in archaea but few in bacteria,
suggesting that the complex is ubiquitous in eukaryotes, and its evolutionary history
began with abundant protein homologs being present in archaea and then a fairly complete
form of the complex emerged in the last eukaryotic common ancestor (LECA). Phylogenetic
analysis indicated that ancient gene duplication and functional divergence of the protein
components of the complex occurred frequently during the evolutionary origin of the LECA
from prokaryotes. We found that such duplications not only increased the complex’s
components but also produced some new functional proteins involved in other nucleolar
functions, such as ribosome biogenesis and even some nonnucleolar (but nuclear) proteins
participating in pre-mRNA splicing, implying the evolutionary emergence of the subnuclear
compartment—the nucleolus—has occurred in the LECA. Therefore, the LECA
harbored not only complicated SSU processomes but also a nucleolus. Our analysis also
revealed that gene duplication, innovation, and loss, caused further divergence of the
complex during the divergence of eukaryotes.
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Affiliation(s)
- Jin-Mei Feng
- State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, Yunnan, China
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15
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Zheng S, Ye K. Purification, crystallization and preliminary X-ray diffraction analysis of Imp3 in complex with an Mpp10 peptide involved in yeast ribosome biogenesis. Acta Crystallogr F Struct Biol Commun 2014; 70:918-21. [PMID: 25005089 PMCID: PMC4089532 DOI: 10.1107/s2053230x14010905] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/21/2014] [Accepted: 05/13/2014] [Indexed: 01/17/2023] Open
Abstract
Eukaryotic ribosome synthesis requires a vast number of transiently associated factors. Mpp10, Imp3 and Imp4 form a protein complex in the 90S pre-ribosomal particle that conducts early processing of 18S rRNA. Here, a short fragment of Mpp10 was identified to associate with and increase the solubility of Imp3. An Imp3-Mpp10 complex was co-expressed, co-purified and co-crystallized. Preliminary X-ray diffraction analysis revealed that the crystal diffracted to 2.1 Å resolution and belonged to space group P2₁2₁2₁, with unit-cell parameters a=51.6, b=86.9, c=88.7 Å.
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Affiliation(s)
- Sanduo Zheng
- Department of Biochemistry and Molecular Biology, College of Life Sciences, Beijing Normal University, Beijing 100875, People’s Republic of China
- National Institute of Biological Sciences, Beijing 102206, People’s Republic of China
| | - Keqiong Ye
- National Institute of Biological Sciences, Beijing 102206, People’s Republic of China
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16
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Sloan KE, Bohnsack MT, Schneider C, Watkins NJ. The roles of SSU processome components and surveillance factors in the initial processing of human ribosomal RNA. RNA (NEW YORK, N.Y.) 2014; 20:540-50. [PMID: 24550520 PMCID: PMC3964915 DOI: 10.1261/rna.043471.113] [Citation(s) in RCA: 52] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/14/2013] [Accepted: 12/19/2013] [Indexed: 05/19/2023]
Abstract
During eukaryotic ribosome biogenesis, three of the mature ribosomal (r)RNAs are released from a single precursor transcript (pre-rRNA) by an ordered series of endonucleolytic cleavages and exonucleolytic processing steps. Production of the 18S rRNA requires the removal of the 5' external transcribed spacer (5'ETS) by endonucleolytic cleavages at sites A0 and A1/site 1. In metazoans, an additional cleavage in the 5'ETS, at site A', upstream of A0, has also been reported. Here, we have investigated how A' processing is coordinated with assembly of the early preribosomal complex. We find that only the tUTP (UTP-A) complex is critical for A' cleavage, while components of the bUTP (UTP-B) and U3 snoRNP are important, but not essential, for efficient processing at this site. All other factors involved in the early stages of 18S rRNA processing that were tested here function downstream from this processing step. Interestingly, we show that the RNA surveillance factors XRN2 and MTR4 are also involved in A' cleavage in humans. A' cleavage is largely bypassed when XRN2 is depleted, and we also discover that A' cleavage is not always the initial processing event in all cell types. Together, our data suggest that A' cleavage is not a prerequisite for downstream pre-rRNA processing steps and may, in fact, represent a quality control step for initial pre-rRNA transcripts. Furthermore, we show that components of the RNA surveillance machinery, including the exosome and TRAMP complexes, also play key roles in the recycling of excised spacer fragments and degradation of aberrant pre-rRNAs in human cells.
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Affiliation(s)
- Katherine E. Sloan
- Institute for Cell and Molecular Biosciences, Newcastle University, Newcastle upon Tyne NE2 4HH, United Kingdom
- Centre for Biochemistry and Molecular Cell Biology, Georg-August University, 37073 Göttingen, Germany
| | - Markus T. Bohnsack
- Centre for Biochemistry and Molecular Cell Biology, Georg-August University, 37073 Göttingen, Germany
| | - Claudia Schneider
- Institute for Cell and Molecular Biosciences, Newcastle University, Newcastle upon Tyne NE2 4HH, United Kingdom
| | - Nicholas J. Watkins
- Institute for Cell and Molecular Biosciences, Newcastle University, Newcastle upon Tyne NE2 4HH, United Kingdom
- Corresponding authorE-mail
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17
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Shah BN, Liu X, Correll CC. Imp3 unfolds stem structures in pre-rRNA and U3 snoRNA to form a duplex essential for small subunit processing. RNA (NEW YORK, N.Y.) 2013; 19:1372-1383. [PMID: 23980203 PMCID: PMC3854528 DOI: 10.1261/rna.039511.113] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 04/09/2013] [Accepted: 06/28/2013] [Indexed: 06/02/2023]
Abstract
Eukaryotic ribosome biogenesis requires rapid hybridization between the U3 snoRNA and the pre-rRNA to direct cleavages at the A0, A1, and A2 sites in pre-rRNA that liberate the small subunit precursor. The bases involved in hybridization of one of the three duplexes that U3 makes with pre-rRNA, designated the U3-18S duplex, are buried in conserved structures: box A/A' stem-loop in U3 snoRNA and helix 1 (H1) in the 18S region of the pre-rRNA. These conserved structures must be unfolded to permit the necessary hybridization. Previously, we reported that Imp3 and Imp4 promote U3-18S hybridization in vitro, but the mechanism by which these proteins facilitate U3-18S duplex formation remained unclear. Here, we directly addressed this question by probing base accessibility with chemical modification and backbone accessibility with ribonuclease activity of U3 and pre-rRNA fragments that mimic the secondary structure observed in vivo. Our results demonstrate that U3-18S hybridization requires only Imp3. Binding to each RNA by Imp3 provides sufficient energy to unfold both the 18S H1 and the U3 box A/A' stem structures. The Imp3 unfolding activity also increases accessibility at the U3-dependent A0 and A1 sites, perhaps signaling cleavage at these sites to generate the 5' mature end of 18S. Imp4 destabilizes the U3-18S duplex to aid U3 release, thus differentiating the roles of these proteins. Protein-dependent unfolding of these structures may serve as a switch to block U3-pre-rRNA interactions until recruitment of Imp3, thereby preventing premature and inaccurate U3-dependent pre-rRNA cleavage and folding events in eukaryotic ribosome biogenesis.
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MESH Headings
- Nucleic Acid Conformation
- Nucleic Acid Hybridization
- RNA Precursors/chemistry
- RNA Precursors/genetics
- RNA Precursors/metabolism
- RNA Processing, Post-Transcriptional
- RNA, Fungal/chemistry
- RNA, Fungal/genetics
- RNA, Fungal/metabolism
- RNA, Ribosomal, 18S/chemistry
- RNA, Ribosomal, 18S/genetics
- RNA, Ribosomal, 18S/metabolism
- RNA, Small Nucleolar/chemistry
- RNA, Small Nucleolar/genetics
- RNA, Small Nucleolar/metabolism
- Ribosomal Proteins/chemistry
- Ribosomal Proteins/genetics
- Ribosomal Proteins/metabolism
- Saccharomyces cerevisiae/genetics
- Saccharomyces cerevisiae/metabolism
- Saccharomyces cerevisiae Proteins/chemistry
- Saccharomyces cerevisiae Proteins/genetics
- Saccharomyces cerevisiae Proteins/metabolism
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Affiliation(s)
- Binal N. Shah
- Department of Biochemistry and Molecular Biology, Rosalind Franklin University of Medicine & Science, North Chicago, Illinois 60064, USA
| | - Xin Liu
- Department of Biochemistry and Molecular Biology, Rosalind Franklin University of Medicine & Science, North Chicago, Illinois 60064, USA
| | - Carl C. Correll
- Department of Biochemistry and Molecular Biology, Rosalind Franklin University of Medicine & Science, North Chicago, Illinois 60064, USA
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18
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Phipps KR, Charette JM, Baserga SJ. The small subunit processome in ribosome biogenesis—progress and prospects. WILEY INTERDISCIPLINARY REVIEWS-RNA 2012; 2:1-21. [PMID: 21318072 DOI: 10.1002/wrna.57] [Citation(s) in RCA: 129] [Impact Index Per Article: 10.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
The small subunit (SSU) processome is a 2.2-MDa ribonucleoprotein complex involved in the processing, assembly, and maturation of the SSU of eukaryotic ribosomes. The identities of many of the factors involved in SSU biogenesis have been elucidated over the past 40 years. However, as our understanding increases, so do the number of questions about the nature of this complicated process. Cataloging the components is the first step toward understanding the molecular workings of a system. This review will focus on how identifying components of ribosome biogenesis has led to the knowledge of how these factors, protein and RNA alike, associate with one another into subcomplexes, with a concentration on the small ribosomal subunit. We will also explore how this knowledge of subcomplex assembly has informed our understanding of the workings of the ribosome synthesis system as a whole.
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Affiliation(s)
- Kathleen R Phipps
- Department of Molecular Biophysics and Biochemistry, Yale University School of Medicine, New Haven, CT, USA
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19
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Marmier-Gourrier N, Cléry A, Schlotter F, Senty-Ségault V, Branlant C. A second base pair interaction between U3 small nucleolar RNA and the 5'-ETS region is required for early cleavage of the yeast pre-ribosomal RNA. Nucleic Acids Res 2011; 39:9731-45. [PMID: 21890904 PMCID: PMC3239212 DOI: 10.1093/nar/gkr675] [Citation(s) in RCA: 48] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
In eukaryotes, U3 snoRNA is essential for pre-rRNA maturation. Its 5'-domain was found to form base pair interactions with the 18S and 5'-ETS parts of the pre-rRNA. In Xenopus laevis, two segments of U3 snoRNA form base-pair interactions with the 5'-ETS region and only one of them is essential to the maturation process. In Saccharomyces cerevisiae, two similar U3 snoRNA-5' ETS interactions are possible; but, the functional importance of only one of them had been tested. Surprisingly, this interaction, which corresponds to the non-essential one in X. laevis, is essential for cell growth and pre-rRNA maturation in yeast. In parallel with [Dutca et al. (2011) The initial U3 snoRNA:pre-rRNA base pairing interaction required for pre-18S rRNA folding revealed by in vivo chemical probing. Nucleic Acids Research, 39, 5164-5180], here we show, that the second possible 11-bp long interaction between the 5' domain of S. cerevisiae U3 snoRNA and the pre-rRNA 5'-ETS region (helix VI) is also essential for pre-rRNA processing and cell growth. Compensatory mutations in one-half of helix VI fully restored cell growth. Only a partial restoration of growth was obtained upon extension of compensatory mutations to the entire helix VI, suggesting sequence requirement for binding of specific proteins. Accordingly, we got strong evidences for a role of segment VI in the association of proteins Mpp10, Imp4 and Imp3.
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Affiliation(s)
- Nathalie Marmier-Gourrier
- Faculté des Sciences et Technologies, Nancy University, UMR AREMS 7214 CNRS-UHP, Boulevard des Aiguillettes, BP70239, 54506 Vandoeuvre-Lès-Nancy cedex, France
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20
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Pérez-Fernández J, Martín-Marcos P, Dosil M. Elucidation of the assembly events required for the recruitment of Utp20, Imp4 and Bms1 onto nascent pre-ribosomes. Nucleic Acids Res 2011; 39:8105-21. [PMID: 21724601 PMCID: PMC3185420 DOI: 10.1093/nar/gkr508] [Citation(s) in RCA: 45] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022] Open
Abstract
The 90S pre-ribosome, also known as the small subunit (SSU) processome, is a large multisubunit particle required for the production of the 18S rRNA from a pre-rRNA precursor. Recently, it has been shown that the formation of this particle entails the initial association of the tUTP subunit with the nascent pre-RNA and, subsequently, the binding of Rrp5/UTP-C and U3 snoRNP/UTP-B subunits in two independent assembly branches. However, the mode of assembly of other 90S pre-ribosome components remains obscure as yet. In this study, we have investigated the assembly of three proteins (Utp20, Imp4 and Bms1) previously regarded as potential nucleating factors of the 90S particle. Here, we demonstrate that the loading of those three proteins onto the pre-rRNA takes place independently of Rrp5/UTP-C and, instead, occurs downstream of the tUTP and U3/UTP-B subcomplexes. We also demonstrate that Bms1 and Utp20 are required for the recruitment of a subset of proteins to nascent pre-ribosomes. Finally, we show that proteins associated through secondary steps condition the stability of the two assembly branches in partially assembled pre-ribosomes. These results provide new information about the functional relationships among 90S particle components and the events that are required for their stepwise incorporation onto the primary pre-rRNA.
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Affiliation(s)
- Jorge Pérez-Fernández
- Centro de Investigación del Cáncer and Instituto de Biología Molecular y Celular del Cáncer, CSIC-University of Salamanca, Campus Unamuno s/n, E37007 Salamanca, Spain
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21
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Cosnier B, Kwapisz M, Hatin I, Namy O, Denmat SHL, Morillon A, Rousset JP, Fabret C. A viable hypomorphic allele of the essential IMP3 gene reveals novel protein functions in Saccharomyces cerevisiae. PLoS One 2011; 6:e19500. [PMID: 21559332 PMCID: PMC3084874 DOI: 10.1371/journal.pone.0019500] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2010] [Accepted: 04/06/2011] [Indexed: 12/31/2022] Open
Abstract
In Saccharomyces cerevisiae, the essential IMP3 gene encodes a component of the SSU processome, a large ribonucleoprotein complex required for processing of small ribosomal subunit RNA precursors. Mutation of the IMP3 termination codon to a sense codon resulted in a viable mutant allele producing a C-terminal elongated form of the Imp3 protein. A strain expressing the mutant allele displayed ribosome biogenesis defects equivalent to IMP3 depletion. This hypomorphic allele represented a unique opportunity to investigate and better understand the Imp3p functions. We demonstrated that the +1 frameshifting was increased in the mutant strain. Further characterizations revealed involvement of the Imp3 protein in DNA repair and telomere length control, pointing to a functional relationship between both pathways and ribosome biogenesis.
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Affiliation(s)
- Bruno Cosnier
- IGM, CNRS, UMR 8621, Orsay, France
- Université Paris-Sud, Orsay, France
| | | | - Isabelle Hatin
- IGM, CNRS, UMR 8621, Orsay, France
- Université Paris-Sud, Orsay, France
| | - Olivier Namy
- IGM, CNRS, UMR 8621, Orsay, France
- Université Paris-Sud, Orsay, France
| | | | | | | | - Céline Fabret
- IGM, CNRS, UMR 8621, Orsay, France
- Université Pierre et Marie Curie, Paris, France
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22
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Lamanna AC, Karbstein K. An RNA conformational switch regulates pre-18S rRNA cleavage. J Mol Biol 2010; 405:3-17. [PMID: 20934433 DOI: 10.1016/j.jmb.2010.09.064] [Citation(s) in RCA: 53] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/19/2010] [Revised: 09/27/2010] [Accepted: 09/29/2010] [Indexed: 12/30/2022]
Abstract
To produce mature ribosomal RNAs (rRNAs), polycistronic rRNA transcripts are cleaved in an ordered series of events. We have uncovered the molecular basis for the ordering of two essential cleavage steps at the 3'-end of 18S rRNA. Using in vitro and in vivo structure probing, RNA binding and cleavage experiments, and yeast genetics, we demonstrate that a conserved RNA sequence in the spacer region between the 18S and 5.8S rRNAs base-pairs with the decoding site of 18S rRNA in early assembly intermediates. Nucleolar cleavage at site A(2) excises this sequence element, leading to a conformational switch in pre-18S rRNA, by which the ribosomal decoding site is formed. This conformational switch positions the nuclease Nob1 for cytoplasmic cleavage at the 3'-end of 18S rRNA and is required for the final maturation step of 18S rRNA in vivo and in vitro. More generally, our data show that the intrinsic ability of RNA to form stable structural switches is exploited to order and regulate RNA-dependent biological processes.
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Affiliation(s)
- Allison C Lamanna
- Department of Chemistry, University of Michigan, Ann Arbor, MI 48109-1055, USA
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23
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Turner AJ, Knox AA, Prieto JL, McStay B, Watkins NJ. A novel small-subunit processome assembly intermediate that contains the U3 snoRNP, nucleolin, RRP5, and DBP4. Mol Cell Biol 2009; 29:3007-17. [PMID: 19332556 PMCID: PMC2682003 DOI: 10.1128/mcb.00029-09] [Citation(s) in RCA: 54] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/07/2009] [Revised: 02/12/2009] [Accepted: 03/24/2009] [Indexed: 11/20/2022] Open
Abstract
Eukaryotic 18S rRNA processing is mediated by the small subunit (SSU) processome, a machine comprised of the U3 small nucleolar RNP (U3 snoRNP), tUTP, bUTP, MPP10, and BMS1/RCL1 subcomplexes. We report that the human SSU processome is a dynamic structure with the recruitment and release of subcomplexes occurring during the early stages of ribosome biogenesis. A novel 50S U3 snoRNP accumulated when either pre-rRNA transcription was blocked or the tUTP proteins were depleted. This complex did not contain the tUTP, bUTP, MPP10, and BMS1/RCL1 subcomplexes but was associated with the RNA-binding proteins nucleolin and RRP5 and the RNA helicase DBP4. Our data suggest that the 50S U3 snoRNP is an SSU assembly intermediate that is likely recruited to the pre-rRNA through the RNA-binding proteins nucleolin and RRP5. We predict that nucleolin is only transiently associated with the SSU processome and likely leaves the complex not long after 50S U3 snoRNP recruitment. The nucleolin-binding site potentially overlaps that of several other key factors, and we propose that this protein must leave the SSU processome for pre-rRNA processing to occur.
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Affiliation(s)
- Amy Jane Turner
- Institute for Cell and Molecular Biosciences, Newcastle University, Newcastle upon Tyne, United Kingdom
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24
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Gérczei T, Shah BN, Manzo AJ, Walter NG, Correll CC. RNA chaperones stimulate formation and yield of the U3 snoRNA-Pre-rRNA duplexes needed for eukaryotic ribosome biogenesis. J Mol Biol 2009; 390:991-1006. [PMID: 19482034 DOI: 10.1016/j.jmb.2009.05.072] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2008] [Revised: 05/26/2009] [Accepted: 05/26/2009] [Indexed: 12/26/2022]
Abstract
Short duplexes between the U3 small nucleolar RNA and the precursor ribosomal RNA must form quickly and with high yield to satisfy the high demand for ribosome synthesis in rapidly growing eukaryotic cells. These interactions, designated the U3-ETS (external transcribed spacer) and U3-18S duplexes, are essential to initiate the processing of small subunit ribosomal RNA. Previously, we showed that duplexes corresponding to those in Saccharomyces cerevisiae are only observed in vitro after addition of one of two proteins: Imp3p or Imp4p. Here, we used fluorescence-based and other in vitro assays to determine whether these proteins possess RNA chaperone activities and to assess whether these activities are sufficient to satisfy the duplex yield and rate requirements expected in vivo. Assembly of both proteins with the U3 small nucleolar RNA into a chaperone complex destabilizes a U3 stem structure, apparently to expose its 18S base-pairing site. As a result, the chaperone complex accelerates formation of the U3-18S duplex from an undetectable rate to one comparable with the intrinsic rate observed for hybridizing short duplexes. The chaperone complex also stabilizes the U3-ETS duplex by 2.7 kcal/mol. These chaperone activities provide high U3-ETS duplex yield and rapid U3-18S duplex formation over a broad concentration range to help ensure that the U3-precursor ribosomal RNA interactions limit neither ribosome biogenesis nor rapid cell growth. The thermodynamic and kinetic framework used is general and thus suitable for investigating the mechanism of action of other RNA chaperones.
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Affiliation(s)
- Tímea Gérczei
- Department of Biochemistry and Molecular Biology, Rosalind Franklin University of Medicine and Science, North Chicago, IL 60064, USA
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25
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Hsieh YC, Tu PJ, Lee YY, Kuo CC, Lin YC, Wu CF, Lin JJ. The U3 small nucleolar ribonucleoprotein component Imp4p is a telomeric DNA-binding protein. Biochem J 2008; 408:387-93. [PMID: 17803460 PMCID: PMC2267362 DOI: 10.1042/bj20070968] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
Abstract
Imp4p is a component of U3 snoRNP (small nucleolar ribonucleoprotein) involved in the maturation of 18S rRNA. We have shown that Imp4p interacts with Cdc13p, a single-stranded telomere-binding protein involved in telomere maintenance. To understand the role of Imp4p in telomeres, we purified recombinant Imp4p protein and tested its binding activity towards telomeric DNA using electrophoretic mobility-shift assays. Our results showed that Imp4p bound specifically to single-stranded telomeric DNA in vitro. The interaction of Imp4p to telomeres in vivo was also demonstrated by chromatin immunoprecipitation experiments. Significantly, the binding of Imp4p to telomeres was not limited to yeast proteins, since the hImp4 (human Imp4) also bound to vertebrate single-stranded telomeric DNA. Thus we conclude that Imp4p is a novel telomeric DNA-binding protein that, in addition to its role in rRNA processing, might participate in telomere function.
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Affiliation(s)
- Yi-Ching Hsieh
- *Institute of Biopharmaceutical Sciences, National Yang-Ming University, Shih-Pai, 112, Taipei, Taiwan, R.O.C
| | - Pei-Jung Tu
- *Institute of Biopharmaceutical Sciences, National Yang-Ming University, Shih-Pai, 112, Taipei, Taiwan, R.O.C
| | - Ying-Yuan Lee
- *Institute of Biopharmaceutical Sciences, National Yang-Ming University, Shih-Pai, 112, Taipei, Taiwan, R.O.C
| | - Chun-Chen Kuo
- †Institute of Biochemistry and Molecular Biology, National Yang-Ming University, Shih-Pai, 112, Taipei, Taiwan, R.O.C
| | - Yi-Chien Lin
- †Institute of Biochemistry and Molecular Biology, National Yang-Ming University, Shih-Pai, 112, Taipei, Taiwan, R.O.C
| | - Chi-Fang Wu
- *Institute of Biopharmaceutical Sciences, National Yang-Ming University, Shih-Pai, 112, Taipei, Taiwan, R.O.C
| | - Jing-Jer Lin
- *Institute of Biopharmaceutical Sciences, National Yang-Ming University, Shih-Pai, 112, Taipei, Taiwan, R.O.C
- †Institute of Biochemistry and Molecular Biology, National Yang-Ming University, Shih-Pai, 112, Taipei, Taiwan, R.O.C
- To whom correspondence should be addressed (email )
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26
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Pérez-Fernández J, Román A, De Las Rivas J, Bustelo XR, Dosil M. The 90S preribosome is a multimodular structure that is assembled through a hierarchical mechanism. Mol Cell Biol 2007; 27:5414-29. [PMID: 17515605 PMCID: PMC1952102 DOI: 10.1128/mcb.00380-07] [Citation(s) in RCA: 139] [Impact Index Per Article: 8.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2007] [Revised: 03/28/2007] [Accepted: 05/10/2007] [Indexed: 02/07/2023] Open
Abstract
The 90S preribosomal particle is required for the production of the 18S rRNA from a pre-rRNA precursor. Despite the identification of the protein components of this particle, its mechanism of assembly and structural design remain unknown. In this work, we have combined biochemical studies, proteomic techniques, and bioinformatic analyses to shed light into the rules of assembly of the yeast 90S preribosome. Our results indicate that several protein subcomplexes work as discrete assembly subunits that bind in defined steps to the 35S pre-rRNA. The assembly of the t-UTP subunit is an essential step for the engagement of at least five additional subunits in two separate, and mutually independent, assembling routes. One of these routes leads to the formation of an assembly intermediate composed of the U3 snoRNP, the Pwp2p/UTP-B, subunit and the Mpp10p complex. The other assembly route involves the stepwise binding of Rrp5p and the UTP-C subunit. We also report the use of a bioinformatic approach that provides a model for the topological arrangement of protein components within the fully assembled particle. Together, our data identify the mechanism of assembly of the 90S preribosome and offer novel information about its internal architecture.
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Affiliation(s)
- Jorge Pérez-Fernández
- Centro de Investigación del Cáncer and Instituto de Biología Molecular y Celular del Cáncer, CSIC-University of Salamanca, Campus Unamuno, E-37007 Salamanca, Spain
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27
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Wang Y, Liu J, Zhao H, Lü W, Zhao J, Yang L, Li N, Du X, Ke Y. Human 1A6/DRIM, the homolog of yeast Utp20, functions in the 18S rRNA processing. BIOCHIMICA ET BIOPHYSICA ACTA-MOLECULAR CELL RESEARCH 2007; 1773:863-8. [PMID: 17498821 DOI: 10.1016/j.bbamcr.2007.04.002] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/23/2006] [Revised: 04/05/2007] [Accepted: 04/05/2007] [Indexed: 11/29/2022]
Abstract
1A6/DRIM is a nucleolar protein with a nucleolar targeting sequence in its 3'-terminus. Bioinformatic analysis indicated that human 1A6/DRIM shares 23% identity and 43% similarity with yeast Utp20, which has been reported as a component of U3 snoRNA protein complex and has been implicated in 18S rRNA processing. In the present study, we found, by utilizing RT-PCR with RNA extracted from anti-1A6/DRIM immunoprecipitates and Northern blotting, that 1A6/DRIM is associated with U3 snoRNA. Pulse-chase labeling assays showed that silencing of 1A6/DRIM expression in HeLa cells resulted in a delayed 18S rRNA processing. Furthermore, immunoprecipitations revealed that 1A6/DRIM was also associated with fibrillarin, another U3 RNP component in HeLa cells. These results indicate that 1A6/DRIM is involved in 18S rRNA processing and is the bona fide mammalian Utp20.
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Affiliation(s)
- You Wang
- Beijing Institute for Cancer Research, School of Oncology, Peking University, 52 Fucheng Road, Beijing 100036, China
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28
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Piekna-Przybylska D, Liu B, Fournier MJ. The U1 snRNA hairpin II as a RNA affinity tag for selecting snoRNP complexes. Methods Enzymol 2007; 425:317-53. [PMID: 17673090 DOI: 10.1016/s0076-6879(07)25014-1] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
When isolating ribonucleoprotein (RNP) complexes by an affinity selection approach, tagging the RNA component can prove to be strategically important. This is especially true for purifying single types of snoRNPs, because in most cases the snoRNA is thought to be the only unique component. Here, we present a general strategy for selecting specific snoRNPs that features a high-affinity tag in the snoRNA and another in a snoRNP core protein. The RNA tag (called U1hpII) is a small (26 nt) stem-loop domain from human U1 snRNA. This structure binds with high affinity (K(D)=10(-11)M) to the RRM domain of the snRNP protein U1A. In our approach, the U1A protein contains a unique affinity tag and is coexpressed in vivo with the tagged snoRNA to yield snoRNP-U1A complexes with two unique protein tags-one in the bound U1A protein and the other in the snoRNP core protein. This scheme has been used effectively to select C/D and H/ACA snoRNPs, including both processing and modifying snoRNPs, and the snoRNA and core proteins are highly enriched. Depending on selection stringency other proteins are isolated as well, including an RNA helicase involved in snoRNP release from pre-rRNA and additional proteins that function in ribosome biogenesis. Tagging the snoRNA component alone is also effective when U1A is expressed with a myc-Tev-protein A fusion sequence. Combined with reduced stringency, enrichment of the U14 snoRNP with this latter system revealed potential interactions with two other snoRNPs, including one processing snoRNP involved in the same cleavages of pre-rRNA.
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29
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Karbstein K, Jonas S, Doudna JA. An essential GTPase promotes assembly of preribosomal RNA processing complexes. Mol Cell 2006; 20:633-43. [PMID: 16307926 DOI: 10.1016/j.molcel.2005.09.017] [Citation(s) in RCA: 64] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/23/2005] [Revised: 08/12/2005] [Accepted: 09/20/2005] [Indexed: 11/26/2022]
Abstract
Ribosome biogenesis in eukaryotes is a highly regulated process involving hundreds of transiently associated proteins and RNAs. Although most of these assembly factors have been genetically linked to specific step(s) in the biogenesis pathway, their biochemical functions are generally unknown. Bms1, an essential protein in yeast, is the only known GTPase required for biosynthesis of the 40S ribosomal subunit and interacts with Rcl1, an essential protein suggested to be an endonuclease. Here, we show thermodynamic coupling in the binding of Bms1 to GTP, Rcl1, and U3 small nucleolar RNA (snoRNA), an essential RNA that base pairs to pre-rRNA. Rcl1 binding to preribosomes is severely limited in yeast cells expressing a Bms1 mutant defective for Rcl1 binding. Additionally, we provide evidence that the C-terminal domain of Bms1 acts as an intramolecular GTPase-activating protein. Together, these data suggest that Bms1 functions as a GTP-regulated switch to deliver Rcl1 to preribosomes, providing molecular insight into preribosome assembly.
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Affiliation(s)
- Katrin Karbstein
- Department of Molecular and Cell Biology, University of California, Berkeley, Berkeley, California 94720, USA
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30
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Borovjagin AV, Gerbi SA. An evolutionary intra-molecular shift in the preferred U3 snoRNA binding site on pre-ribosomal RNA. Nucleic Acids Res 2005; 33:4995-5005. [PMID: 16147982 PMCID: PMC1199564 DOI: 10.1093/nar/gki815] [Citation(s) in RCA: 26] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/04/2022] Open
Abstract
Correct docking of U3 small nucleolar RNA (snoRNA) on pre-ribosomal RNA (pre-rRNA) is essential for rRNA processing to produce 18S rRNA. In this report, we have used Xenopus oocytes to characterize the structural requirements of the U3 snoRNA 3′-hinge interaction with region E1 of the external transcribed spacer (ETS) of pre-rRNA. This interaction is crucial for docking to initiate rRNA processing. 18S rRNA production was inhibited when fewer than 6 of the 8 bp of the U3 3′–hinge complex with the ETS could form; moreover, base pairing involving the right side of the 3′-hinge was more important than the left. Increasing the length of the U3 hinge–ETS interaction by 9 bp impaired rRNA processing. Formation of 18S rRNA was also inhibited by swapping the U3 5′- and 3′-hinge interactions with the ETS or by shifting the base pairing of the U3 3′-hinge to the sequence directly adjacent to ETS region E1. However, 18S rRNA production was partially restored by a compensatory shift that allowed the sequence adjacent to the U3 3′-hinge to pair with the eight bases directly adjacent to ETS region E1. The results suggest that the geometry of the U3 snoRNA interaction with the ETS is critical for rRNA processing.
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MESH Headings
- Animals
- Base Pairing
- Base Sequence
- Binding Sites
- Evolution, Molecular
- Molecular Sequence Data
- Mutation
- RNA Precursors/chemistry
- RNA Precursors/genetics
- RNA Precursors/metabolism
- RNA Processing, Post-Transcriptional
- RNA, Ribosomal, 18S/chemistry
- RNA, Ribosomal, 18S/genetics
- RNA, Ribosomal, 18S/metabolism
- RNA, Small Nucleolar/chemistry
- RNA, Small Nucleolar/genetics
- RNA, Small Nucleolar/metabolism
- Xenopus laevis
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Affiliation(s)
| | - Susan A. Gerbi
- To whom correspondence should be addressed. Tel: +1 401 863 2359; Fax: +1 401 863 1348;
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31
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Ng CL, Waterman D, Koonin EV, Antson AA, Ortiz-Lombardía M. Crystal structure of Mil (Mth680): internal duplication and similarity between the Imp4/Brix domain and the anticodon-binding domain of class IIa aminoacyl-tRNA synthetases. EMBO Rep 2005; 6:140-6. [PMID: 15654320 PMCID: PMC1299238 DOI: 10.1038/sj.embor.7400328] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/06/2004] [Revised: 11/08/2004] [Accepted: 12/03/2004] [Indexed: 11/08/2022] Open
Abstract
Proteins of the Imp4/Brix superfamily are involved in ribosomal RNA processing, an essential function in all cells. We report the first structure of an Imp4/Brix superfamily protein, the Mil (for Methanothermobacter thermautotrophicus Imp4-like) protein (gene product Mth680), from the archaeon M. thermautotrophicus. The amino- and carboxy-terminal halves of Mil show significant structural similarity to one another, suggesting an origin by means of an ancestral duplication. Both halves show the same fold as the anticodon-binding domain of class IIa aminoacyl-tRNA synthetases, with greater conservation seen in the N-terminal half. This structural similarity, together with the charge distribution in Mil, suggests that Imp4/Brix superfamily proteins could bind single-stranded segments of RNA along a concave surface formed by the N-terminal half of their beta-sheet and a central alpha-helix. The crystal structure of Mil is incompatible with the presence, in the Imp4/Brix domain, of a helix-turn-helix motif that was proposed to comprise the RNA-binding moiety of the Imp4/Brix proteins.
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Affiliation(s)
- Chyan Leong Ng
- York Structural Biology Laboratory, Chemistry Department, University of York, York YO10 5YW, UK
| | - David Waterman
- York Structural Biology Laboratory, Chemistry Department, University of York, York YO10 5YW, UK
| | - Eugene V Koonin
- National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, Maryland 20894, USA
| | - Alfred A Antson
- York Structural Biology Laboratory, Chemistry Department, University of York, York YO10 5YW, UK
| | - Miguel Ortiz-Lombardía
- York Structural Biology Laboratory, Chemistry Department, University of York, York YO10 5YW, UK
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