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Janvier A, Hayek H, Alghoul F, Gross L, Allmang C, Martin F, Eriani G. Purification of In Vivo or In Vitro-Assembled RNA-Protein Complexes by RNA Centric Methods. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2024; 3234:17-29. [PMID: 38507197 DOI: 10.1007/978-3-031-52193-5_2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 03/22/2024]
Abstract
Throughout their entire life cycle, RNAs are associated with RNA-binding proteins (RBPs), forming ribonucleoprotein (RNP) complexes with highly dynamic compositions and very diverse functions in RNA metabolism, including splicing, translational regulation, ribosome assembly. Many RNPs remain poorly characterized due to the challenges inherent in their purification and subsequent biochemical characterization. Therefore, developing methods to isolate specific RNA-protein complexes is an important initial step toward understanding their function. Many elegant methodologies have been developed to isolate RNPs. This chapter describes different approaches and methods devised for RNA-specific purification of a target RNP. We focused on general methods for selecting RNPs that target a given RNA under conditions favourable for the copurification of associated factors including RNAs and protein components of the RNP.
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Affiliation(s)
- Aurélie Janvier
- Architecture et Réactivité de l'ARN, Centre National de la Recherche Scientifique, Institut de Biologie Moléculaire et Cellulaire, Université de Strasbourg, Strasbourg, France
| | - Hassan Hayek
- Architecture et Réactivité de l'ARN, Centre National de la Recherche Scientifique, Institut de Biologie Moléculaire et Cellulaire, Université de Strasbourg, Strasbourg, France
| | - Fatima Alghoul
- Architecture et Réactivité de l'ARN, Centre National de la Recherche Scientifique, Institut de Biologie Moléculaire et Cellulaire, Université de Strasbourg, Strasbourg, France
| | - Lauriane Gross
- Architecture et Réactivité de l'ARN, Centre National de la Recherche Scientifique, Institut de Biologie Moléculaire et Cellulaire, Université de Strasbourg, Strasbourg, France
| | - Christine Allmang
- Architecture et Réactivité de l'ARN, Centre National de la Recherche Scientifique, Institut de Biologie Moléculaire et Cellulaire, Université de Strasbourg, Strasbourg, France
| | - Franck Martin
- Architecture et Réactivité de l'ARN, Centre National de la Recherche Scientifique, Institut de Biologie Moléculaire et Cellulaire, Université de Strasbourg, Strasbourg, France
| | - Gilbert Eriani
- Architecture et Réactivité de l'ARN, Centre National de la Recherche Scientifique, Institut de Biologie Moléculaire et Cellulaire, Université de Strasbourg, Strasbourg, France.
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2
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eIF3d is an mRNA cap-binding protein that is required for specialized translation initiation. Nature 2016; 536:96-9. [PMID: 27462815 PMCID: PMC5003174 DOI: 10.1038/nature18954] [Citation(s) in RCA: 231] [Impact Index Per Article: 28.9] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/31/2015] [Accepted: 06/21/2016] [Indexed: 12/19/2022]
Abstract
Eukaryotic mRNAs contain a 5' cap structure critical for recruitment of the translation machinery and initiation of protein synthesis. mRNA recognition is thought to require direct interactions between eukaryotic initiation factor 4E (eIF4E) and the mRNA cap. However, translation of numerous capped mRNAs remains robust during cellular stress, early development, and cell cycle progression1 despite eIF4E inactivation. Here we describe a new cellular cap-dependent pathway of translation initiation that relies on a previously unknown cap-binding activity of eIF3d, a subunit of the 800-kilodalton eukaryotic initiation factor 3 (eIF3) complex. A 1.4 Å crystal structure of the eIF3d cap-binding domain reveals unexpected homology to endonucleases involved in RNA turnover, and allows modeling of cap recognition by eIF3d. eIF3d makes specific contacts to the cap, as exemplified by cap analog competition, and these interactions are essential for assembly of translation initiation complexes on eIF3-specialized mRNAs2 such as the cell proliferation regulator c-Jun. The c-Jun mRNA further encodes an inhibitory RNA element that blocks eIF4E recruitment, thus enforcing alternative cap recognition by eIF3d. Our results reveal a new mechanism of cap-dependent translation independent of eIF4E, and illustrate how modular RNA elements work in concert to direct specialized forms of translation initiation.
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3
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RNA–protein interaction methods to study viral IRES elements. Methods 2015; 91:3-12. [DOI: 10.1016/j.ymeth.2015.06.023] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/15/2015] [Revised: 06/25/2015] [Accepted: 06/30/2015] [Indexed: 12/30/2022] Open
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Othman Z, Sulaiman MK, Willcocks MM, Ulryck N, Blackbourn DJ, Sargueil B, Roberts LO, Locker N. Functional analysis of Kaposi's sarcoma-associated herpesvirus vFLIP expression reveals a new mode of IRES-mediated translation. RNA (NEW YORK, N.Y.) 2014; 20:1803-1814. [PMID: 25246653 PMCID: PMC4201831 DOI: 10.1261/rna.045328.114] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 03/17/2014] [Accepted: 08/26/2014] [Indexed: 06/03/2023]
Abstract
Kaposi's sarcoma-associated herpesvirus (KSHV) is an oncogenic virus, the etiological agent of Kaposi's sarcoma (KS) and primary effusion lymphoma (PEL). One of the key viral proteins that contributes to tumorigenesis is vFLIP, a viral homolog of the FLICE inhibitory protein. This KSHV protein interacts with the NFκB pathway to trigger the expression of antiapoptotic and proinflammatory genes and ultimately leads to tumor formation. The expression of vFLIP is regulated at the translational level by an internal ribosomal entry site (IRES) element. However, the precise mechanism by which ribosomes are recruited internally and the exact location of the IRES has remained elusive. Here we show that a 252-nt fragment directly upstream of vFLIP, within a coding region, directs translation. We have established its RNA structure and demonstrate that IRES activity requires the presence of eIF4A and an intact eIF4G. Furthermore, and unusually for an IRES, eIF4E is part of the complex assembled onto the vFLIP IRES to direct translation. These molecular interactions define a new paradigm for IRES-mediated translation.
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Affiliation(s)
- Zulkefley Othman
- Faculty of Health and Medical Sciences, School of Biosciences and Medicine, University of Surrey, Guildford GU27HE, United Kingdom
| | - Mariam K Sulaiman
- Faculty of Health and Medical Sciences, School of Biosciences and Medicine, University of Surrey, Guildford GU27HE, United Kingdom
| | - Margaret M Willcocks
- Faculty of Health and Medical Sciences, School of Biosciences and Medicine, University of Surrey, Guildford GU27HE, United Kingdom
| | - Nathalie Ulryck
- Faculté des Sciences Pharmaceutiques et Biologiques, UMR8015, Université Paris Descartes, 75270 Paris, France
| | - David J Blackbourn
- Faculty of Health and Medical Sciences, School of Biosciences and Medicine, University of Surrey, Guildford GU27HE, United Kingdom
| | - Bruno Sargueil
- Faculté des Sciences Pharmaceutiques et Biologiques, UMR8015, Université Paris Descartes, 75270 Paris, France
| | - Lisa O Roberts
- Faculty of Health and Medical Sciences, School of Biosciences and Medicine, University of Surrey, Guildford GU27HE, United Kingdom
| | - Nicolas Locker
- Faculty of Health and Medical Sciences, School of Biosciences and Medicine, University of Surrey, Guildford GU27HE, United Kingdom
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5
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Chung L, Bailey D, Leen EN, Emmott EP, Chaudhry Y, Roberts LO, Curry S, Locker N, Goodfellow IG. Norovirus translation requires an interaction between the C Terminus of the genome-linked viral protein VPg and eukaryotic translation initiation factor 4G. J Biol Chem 2014; 289:21738-50. [PMID: 24928504 PMCID: PMC4118132 DOI: 10.1074/jbc.m114.550657] [Citation(s) in RCA: 36] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
Viruses have evolved a variety of mechanisms to usurp the host cell translation machinery to enable translation of the viral genome in the presence of high levels of cellular mRNAs. Noroviruses, a major cause of gastroenteritis in man, have evolved a mechanism that relies on the interaction of translation initiation factors with the virus-encoded VPg protein covalently linked to the 5′ end of the viral RNA. To further characterize this novel mechanism of translation initiation, we have used proteomics to identify the components of the norovirus translation initiation factor complex. This approach revealed that VPg binds directly to the eIF4F complex, with a high affinity interaction occurring between VPg and eIF4G. Mutational analyses indicated that the C-terminal region of VPg is important for the VPg-eIF4G interaction; viruses with mutations that alter or disrupt this interaction are debilitated or non-viable. Our results shed new light on the unusual mechanisms of protein-directed translation initiation.
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Affiliation(s)
- Liliane Chung
- From the Section of Virology, Department of Medicine, Imperial College London, Norfolk Place, London W2 1PG, United Kingdom
| | - Dalan Bailey
- From the Section of Virology, Department of Medicine, Imperial College London, Norfolk Place, London W2 1PG, United Kingdom, School of Immunity and Infection, College of Medical and Dental Sciences, University of Birmingham, Birmingham B15 2TT, United Kingdom
| | - Eoin N Leen
- Department of Life Sciences, Imperial College London, South Kensington, London SW7 2AZ, United Kingdom
| | - Edward P Emmott
- Division of Virology, Department of Pathology, University of Cambridge, Addenbrooke's Hospital, Hills Road, Cambridge CB2 2QQ, United Kingdom, and
| | - Yasmin Chaudhry
- From the Section of Virology, Department of Medicine, Imperial College London, Norfolk Place, London W2 1PG, United Kingdom, Division of Virology, Department of Pathology, University of Cambridge, Addenbrooke's Hospital, Hills Road, Cambridge CB2 2QQ, United Kingdom, and
| | - Lisa O Roberts
- University of Surrey, Faculty of Health and Medical Sciences, School of Biosciences and Medicine, Guildford GU2 7HX, United Kingdom
| | - Stephen Curry
- Department of Life Sciences, Imperial College London, South Kensington, London SW7 2AZ, United Kingdom
| | - Nicolas Locker
- University of Surrey, Faculty of Health and Medical Sciences, School of Biosciences and Medicine, Guildford GU2 7HX, United Kingdom
| | - Ian G Goodfellow
- From the Section of Virology, Department of Medicine, Imperial College London, Norfolk Place, London W2 1PG, United Kingdom, Division of Virology, Department of Pathology, University of Cambridge, Addenbrooke's Hospital, Hills Road, Cambridge CB2 2QQ, United Kingdom, and
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6
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Rapid purification of ribosomal particles assembled on histone H4 mRNA: a new method based on mRNA–DNA chimaeras. Biochem J 2013; 449:719-28. [DOI: 10.1042/bj20121211] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/05/2023]
Abstract
Detailed knowledge of the structure of the ribosomal particles during their assembly on mRNA is a prerequisite for understanding the intricate translation initiation process. In vitro preparation of eukaryotic translation initiation complexes is limited by the rather tricky assembly from individually purified ribosomal subunits, initiation factors and initiator tRNA. In order to directly isolate functional complexes from living cells, methods based on affinity tags have been developed which, however, often suffer from non-specific binding of proteins and/or RNAs. In the present study we present a novel method designed for the purification of high-quality ribosome/mRNA particles assembled in RRL (rabbit reticulocyte lysate). Chimaerical mRNA–DNA molecules, consisting of the full-length mRNA ligated to a biotinylated desoxy-oligonucleotide, are immobilized on streptavidin-coated beads and incubated with RRL to form initiation complexes. After a washing step, the complexes are eluted by specific DNase I digestion of the DNA moiety of the chimaera, releasing initiation complexes in native conditions. Using this simple and robust purification setup, 80S particles properly programmed with full-length histone H4 mRNA were isolated with the expected ribosome/mRNA molar ratio of close to 1. We show that by using this novel approach purified ribosomal particles can be obtained that are suitable for biochemical and structural studies, in particular single-particle cryo-EM (cryo-electron microscopy). This purification method thus is a versatile tool for the isolation of fully functional RNA-binding proteins and macromolecular RNPs.
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Thakor N, Holcik M. IRES-mediated translation of cellular messenger RNA operates in eIF2α- independent manner during stress. Nucleic Acids Res 2011; 40:541-52. [PMID: 21917851 PMCID: PMC3258125 DOI: 10.1093/nar/gkr701] [Citation(s) in RCA: 83] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023] Open
Abstract
Physiological and pathophysiological stress attenuates global translation via phosphorylation of eIF2α. This in turn leads to the reprogramming of gene expression that is required for adaptive stress response. One class of cellular messenger RNAs whose translation was reported to be insensitive to eIF2α phosphorylation-mediated repression of translation is that harboring an Internal Ribosome Entry Site (IRES). IRES-mediated translation of several apoptosis-regulating genes increases in response to hypoxia, serum deprivation or gamma irradiation and promotes tumor cell survival and chemoresistance. However, the molecular mechanism that allows IRES-mediated translation to continue in an eIF2α-independent manner is not known. Here we have used the X-chromosome linked Inhibitor of Apoptosis, XIAP, IRES to address this question. Using toeprinting assay, western blot analysis and polysomal profiling we show that the XIAP IRES supports cap-independent translation when eIF2α is phosphorylated both in vitro and in vivo. During normal growth condition eIF2α-dependent translation on the IRES is preferred. However, IRES-mediated translation switches to eIF5B-dependent mode when eIF2α is phosphorylated as a consequence of cellular stress.
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Affiliation(s)
- Nehal Thakor
- Apoptosis Research Centre, Children's Hospital of Eastern Ontario, 401 Smyth Rd, Ottawa, K1H 8L1, Canada
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Locker N, Chamond N, Sargueil B. A conserved structure within the HIV gag open reading frame that controls translation initiation directly recruits the 40S subunit and eIF3. Nucleic Acids Res 2010; 39:2367-77. [PMID: 21071421 PMCID: PMC3064776 DOI: 10.1093/nar/gkq1118] [Citation(s) in RCA: 64] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022] Open
Abstract
Translation initiation on HIV genomic RNA relies on both cap and Internal Ribosome Entry Site (IRES) dependant mechanisms that are regulated throughout the cell cycle. During a unique phenomenon, the virus recruits initiation complexes through RNA structures located within Gag coding sequence, downstream of the initiation codon. We analyzed initiation complexes paused on the HIV-2 gag IRES and revealed that they contain all the canonical initiation factors except eIF4E and eIF1. We report that eIF3 and the small ribosomal subunit bind HIV RNA within gag open reading frame. We thus propose a novel two step model whereby the initial event is the formation of a ternary eIF3/40S/IRES complex. In a second step, dependent on most of the canonical initiation factors, the complex is rearranged to transfer the ribosome on the initiation codons. The absolute requirement of this large structure for HIV translation defines a new function for a coding region. Moreover, the level of information compaction within this viral genome reveals an additional level of evolutionary constraint on the coding sequence. The conservation of this IRES and its properties in rapidly evolving viruses suggest an important role in the virus life cycle and highlight an attractive new therapeutic target.
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Affiliation(s)
- Nicolas Locker
- Microbial Sciences Division, Faculty of Health and Medical Sciences, University of Surrey - Guildford, Surrey GU2 7HX, UK
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Garlapati S, Wang CC. Giardiavirus internal ribosome entry site has an apparently unique mechanism of initiating translation. PLoS One 2009; 4:e7435. [PMID: 19826476 PMCID: PMC2757703 DOI: 10.1371/journal.pone.0007435] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/20/2009] [Accepted: 09/12/2009] [Indexed: 01/27/2023] Open
Abstract
Giardiavirus (GLV) utilizes an internal ribosome entry site (IRES) for translation initiation in the early branching eukaryote Giardia lamblia. Unlike most of the viral IRESs among higher eukaryotes, which localize primarily within the 5'-untranslated region (UTR), the GLV IRES comprises 253 nts of 5'UTR and the initial 264 nts in the open-reading-frame (ORF). To test if GLV IRES also functions in higher eukaryotic systems, we examined it in rabbit reticulocyte lysate (RRL) and found that it functions much less efficiently than the IRES from the Encephalomyocarditis virus (EMCV) or Cricket paralysis virus (CrPV). In contrast, both EMCV-IRES and CrPV-IRESs were inactive in transfected Giardia cells. Structure-function analysis indicated that only the stem-loop U5 from the 5'UTR and the stem-loop I plus the downstream box (Dbox) from the ORF of GLV IRES are required for limited IRES function in RRL. Edeine, a translation initiation inhibitor, did not significantly affect the function of GLV IRES in either RRL or Giardia, indicating that a pre-initiation complex is not required for GLV IRES-mediated translation initiation. However, the small ribosomal subunit purified from Giardia did not bind to GLV IRES, indicating that additional protein factors may be necessary. A member of the helicase family IBP1 and two known viral IRES binding proteins La autoantigen and SRp20 have been identified in Giardia that bind to GLV IRES in vitro. These three proteins could be involved in facilitating small ribosome recruitment for initiating translation.
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Affiliation(s)
- Srinivas Garlapati
- Department of Pharmaceutical Chemistry, University of California San Francisco, San Francisco, California, United States of America
| | - Ching C. Wang
- Department of Pharmaceutical Chemistry, University of California San Francisco, San Francisco, California, United States of America
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10
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Said N, Rieder R, Hurwitz R, Deckert J, Urlaub H, Vogel J. In vivo expression and purification of aptamer-tagged small RNA regulators. Nucleic Acids Res 2009; 37:e133. [PMID: 19726584 PMCID: PMC2777422 DOI: 10.1093/nar/gkp719] [Citation(s) in RCA: 74] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022] Open
Abstract
Small non-coding RNAs (sRNAs) are an emerging class of post-transcriptional regulators of bacterial gene expression. To study sRNAs and their potential protein interaction partners, it is desirable to purify sRNAs from cells in their native form. Here, we used RNA-based affinity chromatography to purify sRNAs following their expression as aptamer-tagged variants in vivo. To this end, we developed a family of plasmids to express sRNAs with any of three widely used aptamer sequences (MS2, boxB, eIF4A), and systematically tested how the aptamer tagging impacted on intracellular accumulation and target regulation of the Salmonella GcvB, InvR or RybB sRNAs. In addition, we successfully tagged the chromosomal rybB gene with MS2 to observe that RybB-MS2 is fully functional as an envelope stress-induced repressor of ompN mRNA following induction of sigmaE. We further demonstrate that the common sRNA-binding protein, Hfq, co-purifies with MS2-tagged sRNAs of Salmonella. The presented affinity purification strategy may facilitate the isolation of in vivo assembled sRNA–protein complexes in a wide range of bacteria.
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Affiliation(s)
- Nelly Said
- RNA Biology Group, Max Planck Institute for Infection Biology, Charitéplatz 1, 10117 Berlin, Germany
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Easton LE, Locker N, Lukavsky PJ. Conserved functional domains and a novel tertiary interaction near the pseudoknot drive translational activity of hepatitis C virus and hepatitis C virus-like internal ribosome entry sites. Nucleic Acids Res 2009; 37:5537-49. [PMID: 19596815 PMCID: PMC2760816 DOI: 10.1093/nar/gkp588] [Citation(s) in RCA: 34] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/05/2023] Open
Abstract
The translational activity of the hepatitis C virus (HCV) internal ribosome entry site (IRES) and other HCV-like IRES RNAs depends on structured RNA elements in domains II and III, which serve to recruit the ribosomal 40S subunit, eukaryotic initiation factor (eIF) 3 and the ternary eIF2/Met-tRNAiMet/GTP complex and subsequently domain II assists subunit joining. Porcine teschovirus-1 talfan (PTV-1) is a member of the Picornaviridae family, with a predicted HCV-like secondary structure, but only stem-loops IIId and IIIe in the 40S-binding domain display significant sequence conservation with the HCV IRES. Here, we use chemical probing to show that interaction sites with the 40S subunit and eIF3 are conserved between HCV and HCV-like IRESs. In addition, we reveal the functional role of a strictly conserved co-variation between a purine–purine mismatch near the pseudoknot (A–A/G) and the loop sequence of domain IIIe (GAU/CA). These nucleotides are involved in a tertiary interaction, which serves to stabilize the pseudoknot structure and correlates with translational efficiency in both the PTV-1 and HCV IRES. Our data demonstrate conservation of functional domains in HCV and HCV-like IRESs including a more complex structure surrounding the pseudoknot than previously assumed.
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Affiliation(s)
- Laura E Easton
- MRC Laboratory of Molecular Biology, Cambridge CB2 0QH, UK
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12
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Locker N, Easton LE, Lukavsky PJ. HCV and CSFV IRES domain II mediate eIF2 release during 80S ribosome assembly. EMBO J 2007; 26:795-805. [PMID: 17255934 PMCID: PMC1794401 DOI: 10.1038/sj.emboj.7601549] [Citation(s) in RCA: 123] [Impact Index Per Article: 7.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/11/2006] [Accepted: 12/15/2006] [Indexed: 01/11/2023] Open
Abstract
Internal ribosome entry site (IRES) RNAs from the hepatitis C virus (HCV) and classical swine fever virus (CSFV) coordinate cap-independent assembly of eukaryotic 48S initiation complexes, consisting of the 40S ribosomal subunit, eukaryotic initiation factor (eIF) 3 and the eIF2/GTP/Met-tRNA(i)(Met) ternary complex. Here, we report that these IRESes also play a functional role during 80S ribosome assembly downstream of 48S complex formation, in promoting eIF5-induced GTP hydrolysis and eIF2/GDP release from the initiation complex. We show that this function is encoded in their independently folded IRES domain II and that it depends both on its characteristic bent conformation and two conserved RNA motifs, an apical hairpin loop and a loop E. Our data suggest a general mode of subunit joining in HCV and HCV-like IRESes.
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Affiliation(s)
- Nicolas Locker
- MRC Laboratory of Molecular Biology, Hills Road, Cambridge CB2 2QH, UK
| | - Laura E Easton
- MRC Laboratory of Molecular Biology, Hills Road, Cambridge CB2 2QH, UK
| | - Peter J Lukavsky
- MRC Laboratory of Molecular Biology, Hills Road, Cambridge CB2 2QH, UK
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Locker N, Lukavsky PJ. A practical approach to isolate 48S complexes: affinity purification and analyses. Methods Enzymol 2007; 429:83-104. [PMID: 17913620 DOI: 10.1016/s0076-6879(07)29005-6] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Abstract
In vitro assembly of eukaryotic translation initiation complexes requires purification of ribosomal subunits, eukaryotic initiation factors, and initiator tRNA from natural sources and therefore yields only limited material for functional and structural studies. In this chapter, we describe a robust, affinity chromatography-based method for the isolation of eukaryotic 48S initiation complexes from rabbit reticulocyte lysate (RRL). Both canonical and internal ribosome entry site (IRES)-containing mRNAs labeled with a streptomycin aptamer sequence at the 3' end can be used to purify milligram quantities of 48S particles in a simple, two-step procedure. The 48S complexes purified with this method are properly assembled at the initiation codon, contain the expected RNA and protein components in a 1:1 stoichiometry, and are functional intermediates along the initiation pathway.
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Affiliation(s)
- Nicolas Locker
- MRC Laboratory of Molecular Biology, Cambridge, United Kingdom
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