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Sandal S, Singh S, Bansal G, Kaur R, Mogilicherla K, Pandher S, Roy A, Kaur G, Rathore P, Kalia A. Nanoparticle-Shielded dsRNA Delivery for Enhancing RNAi Efficiency in Cotton Spotted Bollworm Earias vittella (Lepidoptera: Nolidae). Int J Mol Sci 2023; 24:ijms24119161. [PMID: 37298113 DOI: 10.3390/ijms24119161] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/12/2023] [Revised: 05/15/2023] [Accepted: 05/18/2023] [Indexed: 06/12/2023] Open
Abstract
The spotted bollworm Earias vittella (Lepidoptera: Nolidae) is a polyphagous pest with enormous economic significance, primarily affecting cotton and okra. However, the lack of gene sequence information on this pest has a significant constraint on molecular investigations and the formulation of superior pest management strategies. An RNA-seq-based transcriptome study was conducted to alleviate such limitations, and de novo assembly was performed to obtain transcript sequences of this pest. Reference gene identification across E. vittella developmental stages and RNAi treatments were conducted using its sequence information, which resulted in identifying transcription elongation factor (TEF), V-type proton ATPase (V-ATPase), and Glyceraldehyde -3-phosphate dehydrogenase (GAPDH) as the most suitable reference genes for normalization in RT-qPCR-based gene expression studies. The present study also identified important developmental, RNAi pathway, and RNAi target genes and performed life-stage developmental expression analysis using RT-qPCR to select the optimal targets for RNAi. We found that naked dsRNA degradation in the E. vittella hemolymph is the primary reason for poor RNAi. A total of six genes including Juvenile hormone methyl transferase (JHAMT), Chitin synthase (CHS), Aminopeptidase (AMN), Cadherin (CAD), Alpha-amylase (AMY), and V-type proton ATPase (V-ATPase) were selected and knocked down significantly with three different nanoparticles encapsulated dsRNA conjugates, i.e., Chitosan-dsRNA, carbon quantum dots-dsRNA (CQD-dsRNA), and Lipofectamine-dsRNA conjugate. These results demonstrate that feeding nanoparticle-shielded dsRNA silences target genes and suggests that nanoparticle-based RNAi can efficiently manage this pest.
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Affiliation(s)
- Shelja Sandal
- Regional Research Station, Punjab Agricultural University, Faridkot 151203, Punjab, India
- Pharmaceutical Sciences and Drug Research, Punjabi University, Patiala 140072, Punjab, India
| | - Satnam Singh
- Regional Research Station, Punjab Agricultural University, Faridkot 151203, Punjab, India
| | - Gulshan Bansal
- Pharmaceutical Sciences and Drug Research, Punjabi University, Patiala 140072, Punjab, India
| | - Ramandeep Kaur
- Regional Research Station, Punjab Agricultural University, Faridkot 151203, Punjab, India
| | - Kanakachari Mogilicherla
- Faculty of Forestry and Wood Sciences, Czech University of Life Sciences Prague, Kamýcká 129, 165 21 Praha, Czech Republic
| | - Suneet Pandher
- Regional Research Station, Punjab Agricultural University, Faridkot 151203, Punjab, India
| | - Amit Roy
- Faculty of Forestry and Wood Sciences, Czech University of Life Sciences Prague, Kamýcká 129, 165 21 Praha, Czech Republic
| | - Gurmeet Kaur
- Regional Research Station, Punjab Agricultural University, Faridkot 151203, Punjab, India
| | - Pankaj Rathore
- Regional Research Station, Punjab Agricultural University, Faridkot 151203, Punjab, India
| | - Anu Kalia
- Electron Microscopy and Nanoscience Laboratory, Punjab Agricultural University, Ludhiana 141004, Punjab, India
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2
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Miller SC, MacDonald CC, Kellogg MK, Karamysheva ZN, Karamyshev AL. Specialized Ribosomes in Health and Disease. Int J Mol Sci 2023; 24:ijms24076334. [PMID: 37047306 PMCID: PMC10093926 DOI: 10.3390/ijms24076334] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2023] [Revised: 03/21/2023] [Accepted: 03/23/2023] [Indexed: 03/30/2023] Open
Abstract
Ribosomal heterogeneity exists within cells and between different cell types, at specific developmental stages, and occurs in response to environmental stimuli. Mounting evidence supports the existence of specialized ribosomes, or specific changes to the ribosome that regulate the translation of a specific group of transcripts. These alterations have been shown to affect the affinity of ribosomes for certain mRNAs or change the cotranslational folding of nascent polypeptides at the exit tunnel. The identification of specialized ribosomes requires evidence of the incorporation of different ribosomal proteins or of modifications to rRNA and/or protein that lead(s) to physiologically relevant changes in translation. In this review, we summarize ribosomal heterogeneity and specialization in mammals and discuss their relevance to several human diseases.
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Affiliation(s)
- Sarah C. Miller
- Department of Cell Biology and Biochemistry, Texas Tech University Health Sciences Center, Lubbock, TX 79430, USA
| | - Clinton C. MacDonald
- Department of Cell Biology and Biochemistry, Texas Tech University Health Sciences Center, Lubbock, TX 79430, USA
| | - Morgana K. Kellogg
- Department of Cell Biology and Biochemistry, Texas Tech University Health Sciences Center, Lubbock, TX 79430, USA
| | | | - Andrey L. Karamyshev
- Department of Cell Biology and Biochemistry, Texas Tech University Health Sciences Center, Lubbock, TX 79430, USA
- Correspondence: ; Tel.: +1-806-743-4102
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3
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Cheng J, Lau B, Thoms M, Ameismeier M, Berninghausen O, Hurt E, Beckmann R. The nucleoplasmic phase of pre-40S formation prior to nuclear export. Nucleic Acids Res 2022; 50:11924-11937. [PMID: 36321656 PMCID: PMC9723619 DOI: 10.1093/nar/gkac961] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2022] [Revised: 10/04/2022] [Accepted: 10/21/2022] [Indexed: 11/07/2022] Open
Abstract
Biogenesis of the small ribosomal subunit in eukaryotes starts in the nucleolus with the formation of a 90S precursor and ends in the cytoplasm. Here, we elucidate the enigmatic structural transitions of assembly intermediates from human and yeast cells during the nucleoplasmic maturation phase. After dissociation of all 90S factors, the 40S body adopts a close-to-mature conformation, whereas the 3' major domain, later forming the 40S head, remains entirely immature. A first coordination is facilitated by the assembly factors TSR1 and BUD23-TRMT112, followed by re-positioning of RRP12 that is already recruited early to the 90S for further head rearrangements. Eventually, the uS2 cluster, CK1 (Hrr25 in yeast) and the export factor SLX9 associate with the pre-40S to provide export competence. These exemplary findings reveal the evolutionary conserved mechanism of how yeast and humans assemble the 40S ribosomal subunit, but reveal also a few minor differences.
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Affiliation(s)
- Jingdong Cheng
- Gene Center and Department of Biochemistry, University of Munich LMU, Feodor-Lynen-Str. 25, 81377 Munich, Germany,Institutes of Biomedical Sciences, Shanghai Key Laboratory of Medical Epigenetics, International Co-laboratory of Medical Epigenetics and Metabolism (Ministry of Science and Technology), Fudan University, Dong’an Road 131, 200032 Shanghai, China
| | - Benjamin Lau
- BZH, University of Heidelberg, Im Neuenheimer Feld 328, 69120 Heidelberg, Germany
| | - Matthias Thoms
- Gene Center and Department of Biochemistry, University of Munich LMU, Feodor-Lynen-Str. 25, 81377 Munich, Germany
| | - Michael Ameismeier
- Gene Center and Department of Biochemistry, University of Munich LMU, Feodor-Lynen-Str. 25, 81377 Munich, Germany
| | - Otto Berninghausen
- Gene Center and Department of Biochemistry, University of Munich LMU, Feodor-Lynen-Str. 25, 81377 Munich, Germany
| | - Ed Hurt
- Correspondence may also be addressed to Ed Hurt.
| | - Roland Beckmann
- To whom correspondence should be addressed. Tel: +49 89 218076900; Fax: +49 89 218076945;
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4
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Black JJ, Johnson AW. Release of the ribosome biogenesis factor Bud23 from small subunit precursors in yeast. RNA (NEW YORK, N.Y.) 2022; 28:371-389. [PMID: 34934010 PMCID: PMC8848936 DOI: 10.1261/rna.079025.121] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 10/18/2021] [Accepted: 12/10/2021] [Indexed: 06/14/2023]
Abstract
The two subunits of the eukaryotic ribosome are produced through quasi-independent pathways involving the hierarchical actions of numerous trans-acting biogenesis factors and the incorporation of ribosomal proteins. The factors work together to shape the nascent subunits through a series of intermediate states into their functional architectures. One of the earliest intermediates of the small subunit (SSU or 40S) is the SSU processome which is subsequently transformed into the pre-40S intermediate. This transformation is, in part, facilitated by the binding of the methyltransferase Bud23. How Bud23 is released from the resultant pre-40S is not known. The ribosomal proteins Rps0, Rps2, and Rps21, termed the Rps0-cluster proteins, and several biogenesis factors bind the pre-40S around the time that Bud23 is released, suggesting that one or more of these factors could induce Bud23 release. Here, we systematically examined the requirement of these factors for the release of Bud23 from pre-40S particles. We found that the Rps0-cluster proteins are needed but not sufficient for Bud23 release. The atypical kinase/ATPase Rio2 shares a binding site with Bud23 and is thought to be recruited to pre-40S after the Rps0-cluster proteins. Depletion of Rio2 prevented the release of Bud23 from the pre-40S. More importantly, the addition of recombinant Rio2 to pre-40S particles affinity-purified from Rio2-depleted cells was sufficient for Bud23 release in vitro. The ability of Rio2 to displace Bud23 was independent of nucleotide hydrolysis. We propose a novel role for Rio2 in which its binding to the pre-40S actively displaces Bud23 from the pre-40S.
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Affiliation(s)
- Joshua J Black
- Department of Molecular Biosciences, The University of Texas at Austin, Austin, Texas 78712, USA
| | - Arlen W Johnson
- Department of Molecular Biosciences, The University of Texas at Austin, Austin, Texas 78712, USA
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5
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Vanden Broeck A, Klinge S. An emerging mechanism for the maturation of the Small Subunit Processome. Curr Opin Struct Biol 2022; 73:102331. [PMID: 35176592 DOI: 10.1016/j.sbi.2022.102331] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/11/2021] [Revised: 12/14/2021] [Accepted: 01/10/2022] [Indexed: 12/15/2022]
Abstract
The biogenesis of the eukaryotic ribosome is a tightly regulated and energetically demanding process involving more than 200 ribosome assembly factors. These factors work in concert to ensure accurate assembly and maturation of both ribosomal subunits. Cryo-electron microscopy (cryo-EM) structures of numerous eukaryotic ribosome assembly intermediates have provided a wealth of structural insights highlighting the molecular interplay of a cast of assembly factors. In this review, we focus on recently determined structures of maturing small subunit (SSU) processomes, giant precursors of the small ribosomal subunit. Based on these structures and complementary biochemical and genetic studies, we discuss an emerging mechanism involving exosome-mediated SSU processome maturation and disassembly.
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Affiliation(s)
- Arnaud Vanden Broeck
- Laboratory of Protein and Nucleic Acid Chemistry, The Rockefeller University, New York, NY 10065, USA. https://twitter.com/AVBroeck
| | - Sebastian Klinge
- Laboratory of Protein and Nucleic Acid Chemistry, The Rockefeller University, New York, NY 10065, USA.
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6
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Mitterer V, Pertschy B. RNA folding and functions of RNA helicases in ribosome biogenesis. RNA Biol 2022; 19:781-810. [PMID: 35678541 PMCID: PMC9196750 DOI: 10.1080/15476286.2022.2079890] [Citation(s) in RCA: 13] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/07/2022] [Accepted: 05/16/2022] [Indexed: 11/13/2022] Open
Abstract
Eukaryotic ribosome biogenesis involves the synthesis of ribosomal RNA (rRNA) and its stepwise folding into the unique structure present in mature ribosomes. rRNA folding starts already co-transcriptionally in the nucleolus and continues when pre-ribosomal particles further maturate in the nucleolus and upon their transit to the nucleoplasm and cytoplasm. While the approximate order of folding of rRNA subdomains is known, especially from cryo-EM structures of pre-ribosomal particles, the actual mechanisms of rRNA folding are less well understood. Both small nucleolar RNAs (snoRNAs) and proteins have been implicated in rRNA folding. snoRNAs hybridize to precursor rRNAs (pre-rRNAs) and thereby prevent premature folding of the respective rRNA elements. Ribosomal proteins (r-proteins) and ribosome assembly factors might have a similar function by binding to rRNA elements and preventing their premature folding. Besides that, a small group of ribosome assembly factors are thought to play a more active role in rRNA folding. In particular, multiple RNA helicases participate in individual ribosome assembly steps, where they are believed to coordinate RNA folding/unfolding events or the release of proteins from the rRNA. In this review, we summarize the current knowledge on mechanisms of RNA folding and on the specific function of the individual RNA helicases involved. As the yeast Saccharomyces cerevisiae is the organism in which ribosome biogenesis and the role of RNA helicases in this process is best studied, we focused our review on insights from this model organism, but also make comparisons to other organisms where applicable.
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Affiliation(s)
- Valentin Mitterer
- Biochemistry Center, Heidelberg University, Im Neuenheimer Feld 328, Heidelberg, Germany
- BioTechMed-Graz, Graz, Austria
| | - Brigitte Pertschy
- BioTechMed-Graz, Graz, Austria
- Institute of Molecular Biosciences, University of Graz, Humboldtstrasse 50, Graz, Austria
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7
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Abstract
In 46,XY men, testis is determined by a genetic network(s) that both promotes testis formation and represses ovarian development. Disruption of this process results in a lack of testis-determination and affected individuals present with 46,XY gonadal dysgenesis (GD), a part of the spectrum of Disorders/Differences of Sex Development/Determination (DSD). A minority of all cases of GD are associated with pathogenic variants in key players of testis-determination, SRY, SOX9, MAP3K1 and NR5A1. However, most of the cases remain unexplained. Recently, unbiased exome sequencing approaches have revealed new genes and loci that may cause 46,XY GD. We critically evaluate the evidence to support causality of these factors and describe how functional studies are continuing to improve our understanding of genotype-phenotype relationships in genes that are established causes of GD. As genomic data continues to be generated from DSD cohorts, we propose several recommendations to help interpret the data and establish causality.
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Affiliation(s)
- Maëva Elzaiat
- Human Developmental Genetics, Institut Pasteur, Paris, France
| | - Ken McElreavey
- Human Developmental Genetics, Institut Pasteur, Paris, France
| | - Anu Bashamboo
- Human Developmental Genetics, Institut Pasteur, Paris, France.
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8
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McElreavey K, Bashamboo A. Monogenic forms of DSD: An update. Horm Res Paediatr 2021; 96:144-168. [PMID: 34963118 DOI: 10.1159/000521381] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 09/02/2021] [Accepted: 11/18/2021] [Indexed: 11/19/2022] Open
Abstract
DSD encompasses a wide range of pathologies that impact gonad formation, development and function in both 46,XX and 46,XY individuals. The majority of these conditions are considered to be monogenic, although the expression of the phenotype may be influenced by genetic modifiers. Although considered monogenic, establishing the genetic etiology in DSD has been difficult compared to other congenital disorders for a number of reasons including the absence of family cases for classical genetic association studies and the lack of evolutionary conservation of key genetic factors involved in gonad formation. In recent years, the widespread use of genomic sequencing technologies has resulted in multiple genes being identified and proposed as novel monogenic causes of 46,XX and/or 46,XY DSD. In this review, we will focus on the main genomic findings of recent years, which consists of new candidate genes or loci for DSD as well as new reproductive phenotypes associated with genes that are well established to cause DSD. For each gene or loci, we summarise the data that is currently available in favor of or against a role for these genes in DSD or the contribution of genomic variants within well-established genes to a new reproductive phenotype. Based on this analysis we propose a series of recommendations that should aid the interpretation of genomic data and ultimately help to improve the accuracy and yield genetic diagnosis of DSD.
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9
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Black JJ, Johnson AW. Genetics animates structure: leveraging genetic interactions to study the dynamics of ribosome biogenesis. Curr Genet 2021; 67:729-738. [PMID: 33844044 DOI: 10.1007/s00294-021-01187-y] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2021] [Revised: 03/28/2021] [Accepted: 03/29/2021] [Indexed: 11/26/2022]
Abstract
The assembly of eukaryotic ribosomes follows an assembly line-like pathway in which numerous trans-acting biogenesis factors act on discrete pre-ribosomal intermediates to progressively shape the nascent subunits into their final functional architecture. Recent advances in cryo-electron microscopy have led to high-resolution structures of many pre-ribosomal intermediates; however, these static snapshots do not capture the dynamic transitions between these intermediates. To this end, molecular genetics can be leveraged to reveal how the biogenesis factors drive these dynamic transitions. Here, we briefly review how we recently used the deletion of BUD23 (bud23∆) to understand its role in the assembly of the ribosomal small subunit. The strong growth defect of bud23∆ mutants places a selective pressure on yeast cells for the occurrence of extragenic suppressors that define a network of functional interactions among biogenesis factors. Mapping these suppressing mutations to recently published structures of pre-ribosomal complexes allowed us to contextualize these suppressing mutations and derive a detailed model in which Bud23 promotes a critical transition event to facilitate folding of the central pseudoknot of the small subunit. This mini-review highlights how genetics can be used to understand the dynamics of complex structures, such as the maturing ribosome.
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Affiliation(s)
- Joshua J Black
- Department of Molecular Biosciences, The University of Texas at Austin, Austin, TX, USA
| | - Arlen W Johnson
- Department of Molecular Biosciences, The University of Texas at Austin, Austin, TX, USA.
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10
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Lau B, Cheng J, Flemming D, La Venuta G, Berninghausen O, Beckmann R, Hurt E. Structure of the Maturing 90S Pre-ribosome in Association with the RNA Exosome. Mol Cell 2020; 81:293-303.e4. [PMID: 33326748 DOI: 10.1016/j.molcel.2020.11.009] [Citation(s) in RCA: 25] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/10/2020] [Revised: 10/01/2020] [Accepted: 11/04/2020] [Indexed: 12/12/2022]
Abstract
Ribosome assembly is catalyzed by numerous trans-acting factors and coupled with irreversible pre-rRNA processing, driving the pathway toward mature ribosomal subunits. One decisive step early in this progression is removal of the 5' external transcribed spacer (5'-ETS), an RNA extension at the 18S rRNA that is integrated into the huge 90S pre-ribosome structure. Upon endo-nucleolytic cleavage at an internal site, A1, the 5'-ETS is separated from the 18S rRNA and degraded. Here we present biochemical and cryo-electron microscopy analyses that depict the RNA exosome, a major 3'-5' exoribonuclease complex, in a super-complex with the 90S pre-ribosome. The exosome is docked to the 90S through its co-factor Mtr4 helicase, a processive RNA duplex-dismantling helicase, which strategically positions the exosome at the base of 5'-ETS helices H9-H9', which are dislodged in our 90S-exosome structures. These findings suggest a direct role of the exosome in structural remodeling of the 90S pre-ribosome to drive eukaryotic ribosome synthesis.
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Affiliation(s)
- Benjamin Lau
- Heidelberg University Biochemistry Center (BZH), Im Neuenheimer Feld 328, 69120 Heidelberg, Germany
| | - Jingdong Cheng
- Gene Center, Department of Biochemistry and Center for Integrated Protein Science Munich (CiPSM), Ludwig-Maximilians-Universität München, Feodor-Lynen-Straße 25, 81377 Munich, Germany
| | - Dirk Flemming
- Heidelberg University Biochemistry Center (BZH), Im Neuenheimer Feld 328, 69120 Heidelberg, Germany
| | - Giuseppe La Venuta
- Heidelberg University Biochemistry Center (BZH), Im Neuenheimer Feld 328, 69120 Heidelberg, Germany
| | - Otto Berninghausen
- Gene Center, Department of Biochemistry and Center for Integrated Protein Science Munich (CiPSM), Ludwig-Maximilians-Universität München, Feodor-Lynen-Straße 25, 81377 Munich, Germany
| | - Roland Beckmann
- Gene Center, Department of Biochemistry and Center for Integrated Protein Science Munich (CiPSM), Ludwig-Maximilians-Universität München, Feodor-Lynen-Straße 25, 81377 Munich, Germany.
| | - Ed Hurt
- Heidelberg University Biochemistry Center (BZH), Im Neuenheimer Feld 328, 69120 Heidelberg, Germany.
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11
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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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12
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Du Y, An W, Zhu X, Sun Q, Qi J, Ye K. Cryo-EM structure of 90 S small ribosomal subunit precursors in transition states. Science 2020; 369:1477-1481. [PMID: 32943522 DOI: 10.1126/science.aba9690] [Citation(s) in RCA: 33] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/10/2020] [Accepted: 07/13/2020] [Indexed: 11/02/2022]
Abstract
The 90S preribosome is a large, early assembly intermediate of small ribosomal subunits that undergoes structural changes to give a pre-40S ribosome. Here, we gained insight into this transition by determining cryo-electron microscopy structures of Saccharomyces cerevisiae intermediates in the path from the 90S to the pre-40S The full transition is blocked by deletion of RNA helicase Dhr1. A series of structural snapshots revealed that the excised 5' external transcribed spacer (5' ETS) is degraded within 90S, driving stepwise disassembly of assembly factors and ribosome maturation. The nuclear exosome, an RNA degradation machine, docks on the 90S through helicase Mtr4 and is primed to digest the 3' end of the 5' ETS. The structures resolved between 3.2- and 8.6-angstrom resolution reveal key intermediates and the critical role of 5' ETS degradation in 90S progression.
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Affiliation(s)
- Yifei Du
- Key Laboratory of RNA Biology, CAS Center for Excellence in Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing 100101, China
| | - Weidong An
- Key Laboratory of RNA Biology, CAS Center for Excellence in Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing 100101, China
| | - Xing Zhu
- Key Laboratory of RNA Biology, CAS Center for Excellence in Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing 100101, China
| | - Qi Sun
- Key Laboratory of RNA Biology, CAS Center for Excellence in Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing 100101, China.,National Institute of Biological Sciences, Beijing 102206, China
| | - Jia Qi
- Key Laboratory of RNA Biology, CAS Center for Excellence in Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing 100101, China.,National Institute of Biological Sciences, Beijing 102206, China.,Department of Biochemistry and Molecular Biology, College of Life Sciences, Beijing Normal University, Beijing 100875, 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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13
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Cheng J, Lau B, La Venuta G, Ameismeier M, Berninghausen O, Hurt E, Beckmann R. 90 S pre-ribosome transformation into the primordial 40 S subunit. Science 2020; 369:1470-1476. [PMID: 32943521 DOI: 10.1126/science.abb4119] [Citation(s) in RCA: 40] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/21/2020] [Accepted: 07/10/2020] [Indexed: 12/25/2022]
Abstract
Production of small ribosomal subunits initially requires the formation of a 90S precursor followed by an enigmatic process of restructuring into the primordial pre-40S subunit. We elucidate this process by biochemical and cryo-electron microscopy analysis of intermediates along this pathway in yeast. First, the remodeling RNA helicase Dhr1 engages the 90S pre-ribosome, followed by Utp24 endonuclease-driven RNA cleavage at site A1, thereby separating the 5'-external transcribed spacer (ETS) from 18S ribosomal RNA. Next, the 5'-ETS and 90S assembly factors become dislodged, but this occurs sequentially, not en bloc. Eventually, the primordial pre-40S emerges, still retaining some 90S factors including Dhr1, now ready to unwind the final small nucleolar U3-18S RNA hybrid. Our data shed light on the elusive 90S to pre-40S transition and clarify the principles of assembly and remodeling of large ribonucleoproteins.
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Affiliation(s)
- Jingdong Cheng
- Gene Center, Department of Biochemistry, University of Munich, 81377 Munich, Germany
| | - Benjamin Lau
- Biochemistry Center (BZH), University of Heidelberg, 69120 Heidelberg, Germany
| | - Giuseppe La Venuta
- Biochemistry Center (BZH), University of Heidelberg, 69120 Heidelberg, Germany
| | - Michael Ameismeier
- Gene Center, Department of Biochemistry, University of Munich, 81377 Munich, Germany
| | - Otto Berninghausen
- Gene Center, Department of Biochemistry, University of Munich, 81377 Munich, Germany
| | - Ed Hurt
- Biochemistry Center (BZH), University of Heidelberg, 69120 Heidelberg, Germany.
| | - Roland Beckmann
- Gene Center, Department of Biochemistry, University of Munich, 81377 Munich, Germany.
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Roychowdhury A, Joret C, Bourgeois G, Heurgué-Hamard V, Lafontaine DLJ, Graille M. The DEAH-box RNA helicase Dhr1 contains a remarkable carboxyl terminal domain essential for small ribosomal subunit biogenesis. Nucleic Acids Res 2019; 47:7548-7563. [PMID: 31188444 PMCID: PMC6698733 DOI: 10.1093/nar/gkz529] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/23/2019] [Revised: 05/28/2019] [Accepted: 06/03/2019] [Indexed: 01/02/2023] Open
Abstract
Ribosome biogenesis is an essential process in all living cells, which entails countless highly sequential and dynamic structural reorganization events. These include formation of dozens RNA helices through Watson-Crick base-pairing within ribosomal RNAs (rRNAs) and between rRNAs and small nucleolar RNAs (snoRNAs), transient association of hundreds of proteinaceous assembly factors to nascent precursor (pre-)ribosomes, and stable assembly of ribosomal proteins. Unsurprisingly, the largest group of ribosome assembly factors are energy-consuming proteins (NTPases) including 25 RNA helicases in budding yeast. Among these, the DEAH-box Dhr1 is essential to displace the box C/D snoRNA U3 from the pre-rRNAs where it is bound in order to prevent premature formation of the central pseudoknot, a dramatic irreversible long-range interaction essential to the overall folding of the small ribosomal subunit. Here, we report the crystal structure of the Dhr1 helicase module, revealing the presence of a remarkable carboxyl-terminal domain essential for Dhr1 function in ribosome biogenesis in vivo and important for its interaction with its coactivator Utp14 in vitro. Furthermore, we report the functional consequences on ribosome biogenesis of DHX37 (human Dhr1) mutations found in patients suffering from microcephaly and other neurological diseases.
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Affiliation(s)
| | - Clément Joret
- RNA Molecular Biology, ULB Cancer Research Center (U-CRC), Fonds de la Recherche Scientifique (F.R.S.-FNRS), Université Libre de Bruxelles (ULB), B-6041 Charleroi-Gosselies, Belgium
| | | | | | - Denis L J Lafontaine
- RNA Molecular Biology, ULB Cancer Research Center (U-CRC), Fonds de la Recherche Scientifique (F.R.S.-FNRS), Université Libre de Bruxelles (ULB), B-6041 Charleroi-Gosselies, Belgium
| | - Marc Graille
- BIOC, CNRS, Ecole polytechnique, IP Paris, F-91128 Palaiseau, France
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Li KK, Mao CY, Zhang JG, Ma Q, Wang YJ, Liu XH, Bao T, Guo W. Overexpression of U three protein 14a (UTP14a) is associated with poor prognosis of esophageal squamous cell carcinoma. Thorac Cancer 2019; 10:2071-2080. [PMID: 31496055 PMCID: PMC6825924 DOI: 10.1111/1759-7714.13176] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/10/2019] [Revised: 08/06/2019] [Accepted: 08/06/2019] [Indexed: 12/09/2022] Open
Abstract
Background Esophageal squamous cell carcinoma (ESCC) is one of the most aggressive and lethal cancers lacking valid prognostic biomarkers. As an essential component of a large ribonucleoprotein complex, U Three Protein 14a (UTP14a) might play important roles in human tumorigenesis. However, the clinical significance and functions of UTP14a in ESCC still remain unclear. Methods From September 2009 to August 2015, 210 patients with ESCC of the thoracic esophagus underwent thoracoscopic esophagectomy in our institute. The corresponding 210 tissue samples and 30 cancer‐distant mucosa (CDM) samples were tested for UTP14a expression by immunohistochemical staining. The long‐term survival was analyzed by the Kaplan–Meier method and Cox proportional hazards regression analyses. CCK8, cell colony formation, cell cycle, apoptosis, cell invasion, and wound healing assays were carried out with ECA109 cells to evaluate the effects of UTP14a on ESCC in vitro. Results UTP14a was positively expressed in 88.1% (185/210) of the ESCC samples. UTP14a expression in ESCC was significantly higher than in CDM, as further confirmed by Western blot analysis. High expression of UTP14a in ESCC correlated significantly with tumor invasive depth (pT stage), which predicts poor disease‐free survival and disease‐specific survival, as indicated by the log‐rank test and Cox proportional hazards regression analysis. Additionally, our in vitro experiments further demonstrated that knockdown of UTP14a inhibits cell proliferation and invasion in ECA109 cells. Conclusions Our results suggest that UTP14a is aberrantly expressed in ESCC, plays a critical role in cancer progression and could be a potential prognosis predictor of ESCC.
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Affiliation(s)
- Kun-Kun Li
- Department of Thoracic Surgery, Daping Hospital, Army Medical University, Chongqing, China
| | - Cheng-Yi Mao
- Department of Pathology, Daping Hospital, Army Medical University, Chongqing, China
| | - Jing-Ge Zhang
- Department of Thoracic Surgery, Daping Hospital, Army Medical University, Chongqing, China
| | - Qiang Ma
- Department of Pathology, Daping Hospital, Army Medical University, Chongqing, China
| | - Ying-Jian Wang
- Department of Thoracic Surgery, Daping Hospital, Army Medical University, Chongqing, China
| | - Xue-Hai Liu
- Department of Thoracic Surgery, Daping Hospital, Army Medical University, Chongqing, China
| | - Tao Bao
- Department of Thoracic Surgery, Daping Hospital, Army Medical University, Chongqing, China
| | - Wei Guo
- Department of Thoracic Surgery, Daping Hospital, Army Medical University, Chongqing, China
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16
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Tsr4 Is a Cytoplasmic Chaperone for the Ribosomal Protein Rps2 in Saccharomyces cerevisiae. Mol Cell Biol 2019; 39:MCB.00094-19. [PMID: 31182640 DOI: 10.1128/mcb.00094-19] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2019] [Accepted: 06/03/2019] [Indexed: 01/31/2023] Open
Abstract
Eukaryotic ribosome biogenesis requires the action of approximately 200 trans-acting factors and the incorporation of 79 ribosomal proteins (RPs). The delivery of RPs to preribosomes is a major challenge for the cell because RPs are often highly basic and contain intrinsically disordered regions prone to nonspecific interactions and aggregation. To counteract this, eukaryotes developed dedicated chaperones for certain RPs that promote their solubility and expression, often by binding eukaryote-specific extensions of the RPs. Rps2 (uS5) is a universally conserved RP that assembles into nuclear pre-40S subunits. However, a chaperone for Rps2 had not been identified. Our laboratory previously characterized Tsr4 as a 40S biogenesis factor of unknown function. Here, we report that Tsr4 cotranslationally associates with Rps2. Rps2 harbors a eukaryote-specific N-terminal extension that is critical for its interaction with Tsr4. Moreover, Tsr4 perturbation resulted in decreased Rps2 levels and phenocopied Rps2 depletion. Despite Rps2 joining nuclear pre-40S particles, Tsr4 appears to be restricted to the cytoplasm. Thus, we conclude that Tsr4 is a cytoplasmic chaperone dedicated to Rps2.
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Boneberg FM, Brandmann T, Kobel L, van den Heuvel J, Bargsten K, Bammert L, Kutay U, Jinek M. Molecular mechanism of the RNA helicase DHX37 and its activation by UTP14A in ribosome biogenesis. RNA (NEW YORK, N.Y.) 2019; 25:685-701. [PMID: 30910870 PMCID: PMC6521606 DOI: 10.1261/rna.069609.118] [Citation(s) in RCA: 29] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 11/15/2018] [Accepted: 03/15/2019] [Indexed: 06/09/2023]
Abstract
Eukaryotic ribosome biogenesis is a highly orchestrated process involving numerous assembly factors including ATP-dependent RNA helicases. The DEAH helicase DHX37 (Dhr1 in yeast) is activated by the ribosome biogenesis factor UTP14A to facilitate maturation of the small ribosomal subunit. We report the crystal structure of DHX37 in complex with single-stranded RNA, revealing a canonical DEAH ATPase/helicase architecture complemented by a structurally unique carboxy-terminal domain (CTD). Structural comparisons of the nucleotide-free DHX37-RNA complex with DEAH helicases bound to RNA and ATP analogs reveal conformational changes resulting in a register shift in the bound RNA, suggesting a mechanism for ATP-dependent 3'-5' RNA translocation. We further show that a conserved sequence motif in UTP14A interacts with and activates DHX37 by stimulating its ATPase activity and enhancing RNA binding. In turn, the CTD of DHX37 is required, but not sufficient, for interaction with UTP14A in vitro and is essential for ribosome biogenesis in vivo. Together, these results shed light on the mechanism of DHX37 and the function of UTP14A in controlling its recruitment and activity during ribosome biogenesis.
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Affiliation(s)
| | - Tobias Brandmann
- Department of Biochemistry, University of Zurich, CH-8057 Zurich, Switzerland
| | - Lena Kobel
- Department of Biochemistry, University of Zurich, CH-8057 Zurich, Switzerland
| | - Jasmin van den Heuvel
- Department of Biology, Institute of Biochemistry, ETH Zurich, CH-8093 Zurich, Switzerland
| | - Katja Bargsten
- Department of Biochemistry, University of Zurich, CH-8057 Zurich, Switzerland
| | - Lukas Bammert
- Department of Biology, Institute of Biochemistry, ETH Zurich, CH-8093 Zurich, Switzerland
| | - Ulrike Kutay
- Department of Biology, Institute of Biochemistry, ETH Zurich, CH-8093 Zurich, Switzerland
| | - Martin Jinek
- Department of Biochemistry, University of Zurich, CH-8057 Zurich, Switzerland
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