1
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Tanaka M, Yokoyama T, Saito H, Nishimoto M, Tsuda K, Sotta N, Shigematsu H, Shirouzu M, Iwasaki S, Ito T, Fujiwara T. Boric acid intercepts 80S ribosome migration from AUG-stop by stabilizing eRF1. Nat Chem Biol 2024; 20:605-614. [PMID: 38267667 DOI: 10.1038/s41589-023-01513-0] [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: 02/11/2022] [Accepted: 11/24/2023] [Indexed: 01/26/2024]
Abstract
In response to environmental changes, cells flexibly and rapidly alter gene expression through translational controls. In plants, the translation of NIP5;1, a boric acid diffusion facilitator, is downregulated in response to an excess amount of boric acid in the environment through upstream open reading frames (uORFs) that consist of only AUG and stop codons. However, the molecular details of how this minimum uORF controls translation of the downstream main ORF in a boric acid-dependent manner have remained unclear. Here, by combining ribosome profiling, translation complex profile sequencing, structural analysis with cryo-electron microscopy and biochemical assays, we show that the 80S ribosome assembled at AUG-stop migrates into the subsequent RNA segment, followed by downstream translation initiation, and that boric acid impedes this process by the stable confinement of eukaryotic release factor 1 on the 80S ribosome on AUG-stop. Our results provide molecular insight into translation regulation by a minimum and environment-responsive uORF.
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Affiliation(s)
- Mayuki Tanaka
- Graduate School of Agricultural and Life Sciences, The University of Tokyo, Tokyo, Japan
| | - Takeshi Yokoyama
- RIKEN Center for Biosystems Dynamics Research, Tsurumi-ku, Yokohama, Japan
- Graduate School of Life Sciences, Tohoku University, Sendai, Japan
| | - Hironori Saito
- Graduate School of Frontier Sciences, The University of Tokyo, Kashiwa, Japan
- RIKEN Cluster for Pioneering Research, Wako, Japan
| | - Madoka Nishimoto
- RIKEN Center for Biosystems Dynamics Research, Tsurumi-ku, Yokohama, Japan
| | - Kengo Tsuda
- RIKEN Center for Biosystems Dynamics Research, Tsurumi-ku, Yokohama, Japan
| | - Naoyuki Sotta
- Graduate School of Agricultural and Life Sciences, The University of Tokyo, Tokyo, Japan
| | - Hideki Shigematsu
- RIKEN Center for Biosystems Dynamics Research, Tsurumi-ku, Yokohama, Japan
- Life Science Research Infrastructure Group, RIKEN SPring-8 Center, Sayo, Japan
| | - Mikako Shirouzu
- RIKEN Center for Biosystems Dynamics Research, Tsurumi-ku, Yokohama, Japan
| | - Shintaro Iwasaki
- Graduate School of Frontier Sciences, The University of Tokyo, Kashiwa, Japan.
- RIKEN Cluster for Pioneering Research, Wako, Japan.
| | - Takuhiro Ito
- RIKEN Center for Biosystems Dynamics Research, Tsurumi-ku, Yokohama, Japan.
| | - Toru Fujiwara
- Graduate School of Agricultural and Life Sciences, The University of Tokyo, Tokyo, Japan.
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2
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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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3
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Alghoul F, Laure S, Eriani G, Martin F. Translation inhibitory elements from Hoxa3 and Hoxa11 mRNAs use uORFs for translation inhibition. eLife 2021; 10:e66369. [PMID: 34076576 PMCID: PMC8172242 DOI: 10.7554/elife.66369] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/08/2021] [Accepted: 05/20/2021] [Indexed: 01/20/2023] Open
Abstract
During embryogenesis, Hox mRNA translation is tightly regulated by a sophisticated molecular mechanism that combines two RNA regulons located in their 5'UTR. First, an internal ribosome entry site (IRES) enables cap-independent translation. The second regulon is a translation inhibitory element or TIE, which ensures concomitant cap-dependent translation inhibition. In this study, we deciphered the molecular mechanisms of mouse Hoxa3 and Hoxa11 TIEs. Both TIEs possess an upstream open reading frame (uORF) that is critical to inhibit cap-dependent translation. However, the molecular mechanisms used are different. In Hoxa3 TIE, we identify an uORF which inhibits cap-dependent translation and we show the requirement of the non-canonical initiation factor eIF2D for this process. The mode of action of Hoxa11 TIE is different, it also contains an uORF but it is a minimal uORF formed by an uAUG followed immediately by a stop codon, namely a 'start-stop'. The 'start-stop' sequence is species-specific and in mice, is located upstream of a highly stable stem loop structure which stalls the 80S ribosome and thereby inhibits cap-dependent translation of Hoxa11 main ORF.
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Affiliation(s)
- Fatima Alghoul
- Institut de Biologie Moléculaire et Cellulaire, “Architecture et Réactivité de l’ARN” CNRS UPR9002, Université de StrasbourgStrasbourgFrance
| | - Schaeffer Laure
- Institut de Biologie Moléculaire et Cellulaire, “Architecture et Réactivité de l’ARN” CNRS UPR9002, Université de StrasbourgStrasbourgFrance
| | - Gilbert Eriani
- Institut de Biologie Moléculaire et Cellulaire, “Architecture et Réactivité de l’ARN” CNRS UPR9002, Université de StrasbourgStrasbourgFrance
| | - Franck Martin
- Institut de Biologie Moléculaire et Cellulaire, “Architecture et Réactivité de l’ARN” CNRS UPR9002, Université de StrasbourgStrasbourgFrance
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4
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Tidu A, Janvier A, Schaeffer L, Sosnowski P, Kuhn L, Hammann P, Westhof E, Eriani G, Martin F. The viral protein NSP1 acts as a ribosome gatekeeper for shutting down host translation and fostering SARS-CoV-2 translation. RNA (NEW YORK, N.Y.) 2020; 27:rna.078121.120. [PMID: 33268501 PMCID: PMC7901841 DOI: 10.1261/rna.078121.120] [Citation(s) in RCA: 91] [Impact Index Per Article: 22.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/14/2020] [Accepted: 11/29/2020] [Indexed: 05/10/2023]
Abstract
SARS-CoV-2 coronavirus is responsible for Covid-19 pandemic. In the early phase of infection, the single-strand positive RNA genome is translated into non-structural proteins (NSP). One of the first proteins produced during viral infection, NSP1, binds to the host ribosome and blocks the mRNA entry channel. This triggers translation inhibition of cellular translation. In spite of the presence of NSP1 on the ribosome, viral translation proceeds however. The molecular mechanism of the so-called viral evasion to NSP1 inhibition remains elusive. Here, we confirm that viral translation is maintained in the presence of NSP1. The evasion to NSP1-inhibition is mediated by the cis-acting RNA hairpin SL1 in the 5'UTR of SARS-CoV-2. NSP1-evasion can be transferred on a reporter transcript by SL1 transplantation. The apical part of SL1 is only required for viral translation. We show that NSP1 remains bound on the ribosome during viral translation. We suggest that the interaction between NSP1 and SL1 frees the mRNA accommodation channel while maintaining NSP1 bound to the ribosome. Thus, NSP1 acts as a ribosome gatekeeper, shutting down host translation or fostering SARS-CoV-2 translation depending on the presence of the SL1 5'UTR hairpin. SL1 is also present and necessary for translation of sub-genomic RNAs in the late phase of the infectious program. Consequently, therapeutic strategies targeting SL1 should affect viral translation at early and late stages of infection. Therefore, SL1 might be seen as a genuine 'Achille heel' of the virus.
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Affiliation(s)
- Antonin Tidu
- Institut de Biologie Moleculaire et Cellulaire, Architecture et Reactivite de l ARN CNRS UPR9002, Universite de Strasbourg, 2, allee Konrad Roentgen, F-67084 Strasbourg (France)
| | - Aurelie Janvier
- Institut de Biologie Moleculaire et Cellulaire, Architecture et Reactivite de l ARN CNRS UPR9002, Universite de Strasbourg, 2, allee Konrad Roentgen, F-67084 Strasbourg (France)
| | - Laure Schaeffer
- Institut de Biologie Moleculaire et Cellulaire, Architecture et Reactivite de l ARN CNRS UPR9002, Universite de Strasbourg, 2, allee Konrad Roentgen F-67084 Strasbourg (France)
| | - Piotr Sosnowski
- Institut de Biologie Moleculaire et Cellulaire, Architecture et Reactivite de l ARN CNRS UPR9002, Universite de Strasbourg, 2, allee Konrad Roentgen, F-67084 Strasbourg (France)
| | - Lauriane Kuhn
- Institut de Biologie Moleculaire et Cellulaire, Plateforme Proteomique Strasbourg Esplanade, CNRS FRC1589, Universite de Strasbourg, 2, allee Konrad Roentgen, F-67084 Strasbourg (France)
| | - Philippe Hammann
- Institut de Biologie Moleculaire et Cellulaire, Plateforme Proteomique Strasbourg Esplanade, CNRS FRC1589, Universite de Strasbourg, 2, allee Konrad Roentgen, F-67084 Strasbourg (France)
| | - Eric Westhof
- Institut de Biologie Moleculaire et Cellulaire, Architecture et Reactivite de l ARN CNRS UPR9002, Universite de Strasbourg, 2, allee Konrad Roentgen, F-67084 Strasbourg (France)
| | - Gilbert Eriani
- Institut de Biologie Moleculaire et Cellulaire, Architecture et Reactivite de l ARN CNRS UPR9002, Universite de Strasbourg, 2, allee Konrad Roentgen, F-67084 Strasbourg (France)
| | - Franck Martin
- Institut de Biologie Moleculaire et Cellulaire, Architecture et Reactivite de l ARN CNRS UPR9002, Universite de Strasbourg, 2, allee Konrad Roentgen, F-67084 Strasbourg (France);
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5
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Grad-cryo-EM: Tool to Isolate Translation Initiation Complexes from Rabbit Reticulocyte Lysate Suitable for Structural Studies. Methods Mol Biol 2020. [PMID: 32006323 DOI: 10.1007/978-1-0716-0278-2_21] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register]
Abstract
Since its development, single-particle cryogenic electron microscopy (cryo-EM) has played a central role in the study at medium resolution of both bacterial and eukaryotic ribosomal complexes. With the advent of the direct electron detectors and new processing software which allow obtaining structures at atomic resolution, formerly obtained only by X-ray crystallography, cryo-EM has become the method of choice for the structural analysis of the translation machinery. In most of the cases, the ribosomal complexes at different stages of the translation process are assembled in vitro from purified components, which limit the analysis to previously well-characterized complexes with known factors composition. The initiation phase of the protein synthesis is a very dynamic process during which several proteins interact with the translation apparatus leading to the formation of a chronological series of initiation complexes (ICs). Here we describe a method to isolate ICs assembled on natural in vitro transcribed mRNA directly from rabbit reticulocyte lysate (RRL) by sucrose density gradient centrifugation . The Grad-cryo-EM approach allows investigating structures and composition of intermediate ribosomal complexes prepared in near-native condition by cryo-EM and mass spectrometry analyses. This is a powerful approach, which could be used to study translation initiation of any mRNAs, including IRES containing ones, and which could be adapted to different cell extracts.
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6
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Biotin oligonucleotide labeling reactions: A method to assess their effectiveness and reproducibility. Anal Biochem 2020; 593:113590. [PMID: 31962102 DOI: 10.1016/j.ab.2020.113590] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2019] [Accepted: 01/16/2020] [Indexed: 11/24/2022]
Abstract
The strong molecular interaction between biotin and streptavidin is widely used in the growing field of nucleic acid nanotechnology. Several biotin labeled oligonucleotide tools have been developed for the detection of biological molecules as well as for protein purification. For these reasons, biotinylation can be considered one of the main chemical reactions for nucleic acid labeling. However, despite its widespread application and the presence on the market of many reagents for the conjugation of biotin to oligonucleotides, it is not yet available a cheap, easy and sensitive system able to assess the effectiveness and reproducibility of this reaction. Here, we present an accurate and reliable method to achieve a qualitative and quantitative analysis of oligonucleotide biotinylation. The protocol employs basic laboratory instruments and standard software for molecular biology applications and does not require advanced expertise for its execution. Most importantly, our method is independent from complex kinetic equilibrium parameters and shows a limit of detection more than one order of magnitude lower than the current fluorometric gold standard assay. Therefore, this method could become a standard, inexpensive and routinely used quality test for post-synthesis evaluation of biotin conjugation reactions.
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7
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Mailliot J, Martin F. Viral internal ribosomal entry sites: four classes for one goal. WILEY INTERDISCIPLINARY REVIEWS. RNA 2018; 9. [PMID: 29193740 DOI: 10.1002/wrna.1458] [Citation(s) in RCA: 64] [Impact Index Per Article: 10.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/17/2017] [Revised: 09/19/2017] [Accepted: 10/02/2017] [Indexed: 12/22/2022]
Abstract
To ensure efficient propagation, viruses need to rapidly produce viral proteins after cell entrance. Since viral genomes do not encode any components of the protein biosynthesis machinery, viral proteins must be produced by the host cell. To hi-jack the host cellular translation, viruses use a great variety of distinct strategies. Many single-stranded positive-sensed RNA viruses contain so-called internal ribosome entry sites (IRESs). IRESs are structural RNA motifs that have evolved to specific folds that recruit the host ribosomes on the viral coding sequences in order to synthesize viral proteins. In host canonical translation, recruitment of the translation machinery components is essentially guided by the 5' cap (m7 G) of mRNA. In contrast, IRESs are able to promote efficient ribosome assembly internally and in cap-independent manner. IRESs have been categorized into four classes, based on their length, nucleotide sequence, secondary and tertiary structures, as well as their mode of action. Classes I and II require the assistance of cellular auxiliary factors, the eukaryotic intiation factors (eIF), for efficient ribosome assembly. Class III IRESs require only a subset of eIFs whereas Class IV, which are the more compact, can promote translation without any eIFs. Extensive functional and structural investigations of IRESs over the past decades have allowed a better understanding of their mode of action for viral translation. Because viral translation has a pivotal role in the infectious program, IRESs are therefore attractive targets for therapeutic purposes. WIREs RNA 2018, 9:e1458. doi: 10.1002/wrna.1458 This article is categorized under: Translation > Ribosome Structure/Function Translation > Translation Mechanisms RNA Interactions with Proteins and Other Molecules > RNA-Protein Complexes.
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Affiliation(s)
- Justine Mailliot
- Institut de Génétique et de Biologie Moléculaire et Cellulaire, CNRS UMR7104, INSERM U964, Illkirch-Graffenstaden, France
| | - Franck Martin
- Institut de Biologie Moléculaire et Cellulaire, "Architecture et Réactivité de l'ARN" CNRS UPR9002, Université De Strasbourg, Strasbourg, France
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8
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Gross L, Vicens Q, Einhorn E, Noireterre A, Schaeffer L, Kuhn L, Imler JL, Eriani G, Meignin C, Martin F. The IRES5'UTR of the dicistrovirus cricket paralysis virus is a type III IRES containing an essential pseudoknot structure. Nucleic Acids Res 2017; 45:8993-9004. [PMID: 28911115 PMCID: PMC5587806 DOI: 10.1093/nar/gkx622] [Citation(s) in RCA: 35] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/03/2016] [Accepted: 07/07/2017] [Indexed: 02/02/2023] Open
Abstract
Cricket paralysis virus (CrPV) is a dicistrovirus. Its positive-sense single-stranded RNA genome contains two internal ribosomal entry sites (IRESs). The 5′ untranslated region (5′UTR) IRES5′UTR mediates translation of non-structural proteins encoded by ORF1 whereas the well-known intergenic region (IGR) IRESIGR is required for translation of structural proteins from open reading frame 2 in the late phase of infection. Concerted action of both IRES is essential for host translation shut-off and viral translation. IRESIGR has been extensively studied, in contrast the IRES5′UTR remains largely unexplored. Here, we define the minimal IRES element required for efficient translation initiation in drosophila S2 cell-free extracts. We show that IRES5′UTR promotes direct recruitment of the ribosome on the cognate viral AUG start codon without any scanning step, using a Hepatitis-C virus-related translation initiation mechanism. Mass spectrometry analysis revealed that IRES5′UTR recruits eukaryotic initiation factor 3, confirming that it belongs to type III class of IRES elements. Using Selective 2′-hydroxyl acylation analyzed by primer extension and DMS probing, we established a secondary structure model of 5′UTR and of the minimal IRES5′UTR. The IRES5′UTR contains a pseudoknot structure that is essential for proper folding and ribosome recruitment. Overall, our results pave the way for studies addressing the synergy and interplay between the two IRES from CrPV.
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Affiliation(s)
- Lauriane Gross
- Université de Strasbourg, CNRS, Architecture et Réactivité de l'ARN, UPR 9002, F-67000 Strasbourg, France
| | - Quentin Vicens
- Université de Strasbourg, CNRS, Architecture et Réactivité de l'ARN, UPR 9002, F-67000 Strasbourg, France
| | - Evelyne Einhorn
- Université de Strasbourg, CNRS, Réponse Immunitaire et Développement chez les Insectes, UPR 9022, F-67000 Strasbourg, France
| | - Audrey Noireterre
- Université de Strasbourg, CNRS, Architecture et Réactivité de l'ARN, UPR 9002, F-67000 Strasbourg, France
| | - Laure Schaeffer
- Université de Strasbourg, CNRS, Architecture et Réactivité de l'ARN, UPR 9002, F-67000 Strasbourg, France
| | - Lauriane Kuhn
- Université de Strasbourg, CNRS, Plateforme Protéomique Strasbourg-Esplanade, F-67000 Strasbourg, France
| | - Jean-Luc Imler
- Université de Strasbourg, CNRS, Réponse Immunitaire et Développement chez les Insectes, UPR 9022, F-67000 Strasbourg, France
| | - Gilbert Eriani
- Université de Strasbourg, CNRS, Architecture et Réactivité de l'ARN, UPR 9002, F-67000 Strasbourg, France
| | - Carine Meignin
- Université de Strasbourg, CNRS, Réponse Immunitaire et Développement chez les Insectes, UPR 9022, F-67000 Strasbourg, France
| | - Franck Martin
- Université de Strasbourg, CNRS, Architecture et Réactivité de l'ARN, UPR 9002, F-67000 Strasbourg, France
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9
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Martin F, Ménétret JF, Simonetti A, Myasnikov AG, Vicens Q, Prongidi-Fix L, Natchiar SK, Klaholz BP, Eriani G. Ribosomal 18S rRNA base pairs with mRNA during eukaryotic translation initiation. Nat Commun 2016; 7:12622. [PMID: 27554013 PMCID: PMC4999511 DOI: 10.1038/ncomms12622] [Citation(s) in RCA: 33] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2016] [Accepted: 07/18/2016] [Indexed: 02/07/2023] Open
Abstract
Eukaryotic mRNAs often contain a Kozak sequence that helps tether the ribosome to the AUG start codon. The mRNA of histone H4 (h4) does not undergo classical ribosome scanning but has evolved a specific tethering mechanism. The cryo-EM structure of the rabbit ribosome complex with mouse h4 shows that the mRNA forms a folded, repressive structure at the mRNA entry site on the 40S subunit next to the tip of helix 16 of 18S ribosomal RNA (rRNA). Toe-printing and mutational assays reveal that an interaction exists between a purine-rich sequence in h4 mRNA and a complementary UUUC sequence of helix h16. Together the present data establish that the h4 mRNA harbours a sequence complementary to an 18S rRNA sequence which tethers the mRNA to the ribosome to promote proper start codon positioning, complementing the interactions of the 40S subunit with the Kozak sequence that flanks the AUG start codon. Prokaryotic translation initiation involves mRNA-ribosomal RNA base pairing interactions. Here, the authors provide evidence for a similar base pairing interactions occurring between the human h4 mRNA and helix 16 of the small subunit rRNA to position the correct AUG codon in the decoding site.
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Affiliation(s)
- Franck Martin
- Architecture et Réactivité de l'ARN, Centre National de la Recherche Scientifique (CNRS) UPR9002, Institute of Molecular and Cellular Biology (IBMC), Université de Strasbourg, 15 rue René Descartes, 67084 Strasbourg, France
| | - Jean-François Ménétret
- Department of Integrated Structural Biology, Centre for Integrative Biology (CBI), IGBMC (Institute of Genetics and of Molecular and Cellular Biology), 1 rue Laurent Fries, 67404 Illkirch, France.,CNRS UMR 7104, 67404 Illkirch, France.,Institut National de la Santé et de la Recherche Médicale (INSERM) U964, 67404 Illkirch, France.,Université de Strasbourg, 67081 Strasbourg, France
| | - Angelita Simonetti
- Architecture et Réactivité de l'ARN, Centre National de la Recherche Scientifique (CNRS) UPR9002, Institute of Molecular and Cellular Biology (IBMC), Université de Strasbourg, 15 rue René Descartes, 67084 Strasbourg, France
| | - Alexander G Myasnikov
- Department of Integrated Structural Biology, Centre for Integrative Biology (CBI), IGBMC (Institute of Genetics and of Molecular and Cellular Biology), 1 rue Laurent Fries, 67404 Illkirch, France.,CNRS UMR 7104, 67404 Illkirch, France.,Institut National de la Santé et de la Recherche Médicale (INSERM) U964, 67404 Illkirch, France.,Université de Strasbourg, 67081 Strasbourg, France
| | - Quentin Vicens
- Architecture et Réactivité de l'ARN, Centre National de la Recherche Scientifique (CNRS) UPR9002, Institute of Molecular and Cellular Biology (IBMC), Université de Strasbourg, 15 rue René Descartes, 67084 Strasbourg, France
| | - Lydia Prongidi-Fix
- Architecture et Réactivité de l'ARN, Centre National de la Recherche Scientifique (CNRS) UPR9002, Institute of Molecular and Cellular Biology (IBMC), Université de Strasbourg, 15 rue René Descartes, 67084 Strasbourg, France
| | - S Kundhavai Natchiar
- Department of Integrated Structural Biology, Centre for Integrative Biology (CBI), IGBMC (Institute of Genetics and of Molecular and Cellular Biology), 1 rue Laurent Fries, 67404 Illkirch, France.,CNRS UMR 7104, 67404 Illkirch, France.,Institut National de la Santé et de la Recherche Médicale (INSERM) U964, 67404 Illkirch, France.,Université de Strasbourg, 67081 Strasbourg, France
| | - Bruno P Klaholz
- Department of Integrated Structural Biology, Centre for Integrative Biology (CBI), IGBMC (Institute of Genetics and of Molecular and Cellular Biology), 1 rue Laurent Fries, 67404 Illkirch, France.,CNRS UMR 7104, 67404 Illkirch, France.,Institut National de la Santé et de la Recherche Médicale (INSERM) U964, 67404 Illkirch, France.,Université de Strasbourg, 67081 Strasbourg, France
| | - Gilbert Eriani
- Architecture et Réactivité de l'ARN, Centre National de la Recherche Scientifique (CNRS) UPR9002, Institute of Molecular and Cellular Biology (IBMC), Université de Strasbourg, 15 rue René Descartes, 67084 Strasbourg, France
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10
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Simonetti A, Brito Querido J, Myasnikov AG, Mancera-Martinez E, Renaud A, Kuhn L, Hashem Y. eIF3 Peripheral Subunits Rearrangement after mRNA Binding and Start-Codon Recognition. Mol Cell 2016; 63:206-217. [PMID: 27373335 DOI: 10.1016/j.molcel.2016.05.033] [Citation(s) in RCA: 76] [Impact Index Per Article: 9.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/29/2016] [Revised: 04/07/2016] [Accepted: 05/23/2016] [Indexed: 11/30/2022]
Abstract
mRNA translation initiation in eukaryotes requires the cooperation of a dozen eukaryotic initiation factors (eIFs) forming several complexes, which leads to mRNA attachment to the small ribosomal 40S subunit, mRNA scanning for start codon, and accommodation of initiator tRNA at the 40S P site. eIF3, composed of 13 subunits, 8 core (a, c, e, f, h, l, k, and m) and 5 peripheral (b, d, g, i, and j), plays a central role during this process. Here we report a cryo-electron microscopy structure of a mammalian 48S initiation complex at 5.8 Å resolution. It shows the relocation of subunits eIF3i and eIF3g to the 40S intersubunit face on the GTPase binding site, at a late stage in initiation. On the basis of a previous study, we demonstrate the relocation of eIF3b to the 40S intersubunit face, binding below the eIF2-Met-tRNAi(Met) ternary complex upon mRNA attachment. Our analysis reveals the deep rearrangement of eIF3 and unravels the molecular mechanism underlying eIF3 function in mRNA scanning and timing of ribosomal subunit joining.
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Affiliation(s)
- Angelita Simonetti
- CNRS, Architecture et Réactivité de l'ARN UPR9002, Université de Strasbourg, 67084 Strasbourg, France.
| | - Jailson Brito Querido
- CNRS, Architecture et Réactivité de l'ARN UPR9002, Université de Strasbourg, 67084 Strasbourg, France
| | | | - Eder Mancera-Martinez
- CNRS, Architecture et Réactivité de l'ARN UPR9002, Université de Strasbourg, 67084 Strasbourg, France
| | - Adeline Renaud
- CNRS, Architecture et Réactivité de l'ARN UPR9002, Université de Strasbourg, 67084 Strasbourg, France
| | - Lauriane Kuhn
- CNRS, Proteomic Platform Strasbourg - Esplanade, 67084 Strasbourg, France
| | - Yaser Hashem
- CNRS, Architecture et Réactivité de l'ARN UPR9002, Université de Strasbourg, 67084 Strasbourg, France.
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Chicher J, Simonetti A, Kuhn L, Schaeffer L, Hammann P, Eriani G, Martin F. Purification of mRNA-programmed translation initiation complexes suitable for mass spectrometry analysis. Proteomics 2015; 15:2417-25. [PMID: 25914180 DOI: 10.1002/pmic.201400628] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/28/2014] [Revised: 02/27/2015] [Accepted: 04/21/2015] [Indexed: 12/21/2022]
Abstract
Liquid Chromatography coupled to tandem mass spectrometry (nanoLC-MS/MS) is a powerful analytical technique for the identification and mass analysis of complex protein mixtures. Here, we present a combination of methods developed for the extensive/deep proteomic analysis of purified ribosome/mRNA particles assembled in rabbit reticulocyte lysate (RRL). Ribosomes are assembled on chimeric biotinylated mRNA-DNA molecules immobilized on streptavidin-coated beads and incubated with RRL to form initiation complexes. After washing steps, the complexes are trypsin-digested directly on the beads in semi-native condition or after their elution from the beads in denaturing Laemmli buffer. The nanoLC-MS/MS analysis performed on complexes assembled on β-globin, viral HCV, and histone H4 mRNAs revealed significant differences in initiation factors composition in agreement with models of translation initiation used by these different types of mRNAs. Using Laemmli-denaturing condition induces release of deeply buried peptides from the ribosome and eukaryotic initiation factor 3 (eIF3) allowing the identification of the nearly complete set of ribosomal proteins.
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Affiliation(s)
- Johana Chicher
- Institut de Biologie Moléculaire et Cellulaire, Plateforme Protéomique Strasbourg - Esplanade, Université De Strasbourg, Strasbourg, France
| | - Angelita Simonetti
- Institut de Biologie Moléculaire et Cellulaire, "Architecture et Réactivité de l'ARN", Université De Strasbourg, Strasbourg, France
| | - Lauriane Kuhn
- Institut de Biologie Moléculaire et Cellulaire, Plateforme Protéomique Strasbourg - Esplanade, Université De Strasbourg, Strasbourg, France
| | - Laure Schaeffer
- Institut de Biologie Moléculaire et Cellulaire, "Architecture et Réactivité de l'ARN", Université De Strasbourg, Strasbourg, France
| | - Philippe Hammann
- Institut de Biologie Moléculaire et Cellulaire, Plateforme Protéomique Strasbourg - Esplanade, Université De Strasbourg, Strasbourg, France
| | - Gilbert Eriani
- Institut de Biologie Moléculaire et Cellulaire, "Architecture et Réactivité de l'ARN", Université De Strasbourg, Strasbourg, France
| | - Franck Martin
- Institut de Biologie Moléculaire et Cellulaire, "Architecture et Réactivité de l'ARN", Université De Strasbourg, Strasbourg, France
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Panchapakesan SSS, Jeng SCY, Unrau PJ. RNA complex purification using high-affinity fluorescent RNA aptamer tags. Ann N Y Acad Sci 2015; 1341:149-55. [PMID: 25585661 DOI: 10.1111/nyas.12663] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/01/2022]
Abstract
RNA plays important roles in cellular processes, but RNA-protein complexes are notoriously hard to isolate and study. We compare and contrast existing RNA- and protein-purification strategies with the potential of new RNA-tagging systems such as RNA Spinach and RNA Mango. Each RNA aptamer binds a small fluorophore, resulting in a highly fluorescent complex that is thousands of times brighter than the unbound fluorophore. Provided that the aptamer binding affinity is high enough, derivatized dyes can be used in conjunction with these aptamers to purify RNA complexes while simultaneously using their intrinsic fluorescence to track the complex of interest. The known strengths and weakness of these RNA tagging systems are discussed.
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