1
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Rapone R, Del Maestro L, Bouyioukos C, Albini S, Cruz-Tapias P, Joliot V, Cosson B, Ait-Si-Ali S. The cytoplasmic fraction of the histone lysine methyltransferase Setdb1 is essential for embryonic stem cells. iScience 2023; 26:107386. [PMID: 37559904 PMCID: PMC10407132 DOI: 10.1016/j.isci.2023.107386] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2023] [Revised: 06/26/2023] [Accepted: 07/11/2023] [Indexed: 08/11/2023] Open
Abstract
The major lysine methyltransferase (KMT) Setdb1 is essential for self-renewal and viability of mouse embryonic stem cells (mESCs). Setdb1 was primarily known to methylate the lysine 9 of histone 3 (H3K9) in the nucleus, where it regulates chromatin functions. However, Setdb1 is also massively localized in the cytoplasm, including in mESCs, where its role remains elusive. Here, we show that the cytoplasmic Setdb1 (cSetdb1) is essential for the survival of mESCs. Yeast two-hybrid analysis revealed that cSetdb1 interacts with several regulators of mRNA stability and protein translation machinery, such as the ESCs-specific E3 ubiquitin ligase and mRNA silencer Trim71/Lin41. We found that cSetdb1 is required for the integrity of Trim71 complex(es) involved in mRNA metabolism and translation. cSetdb1 modulates the abundance of mRNAs and the rate of newly synthesized proteins. Altogether, our data uncovered the cytoplasmic post-transcriptional regulation of gene expression mediated by a key epigenetic regulator.
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Affiliation(s)
- Roberta Rapone
- Université Paris Cité, CNRS, Epigenetics and Cell Fate, UMR7216, 75013 Paris, France
| | - Laurence Del Maestro
- Université Paris Cité, CNRS, Epigenetics and Cell Fate, UMR7216, 75013 Paris, France
| | - Costas Bouyioukos
- Université Paris Cité, CNRS, Epigenetics and Cell Fate, UMR7216, 75013 Paris, France
| | - Sonia Albini
- Université Paris Cité, CNRS, Epigenetics and Cell Fate, UMR7216, 75013 Paris, France
| | - Paola Cruz-Tapias
- Université Paris Cité, CNRS, Epigenetics and Cell Fate, UMR7216, 75013 Paris, France
| | - Véronique Joliot
- Université Paris Cité, CNRS, Epigenetics and Cell Fate, UMR7216, 75013 Paris, France
| | - Bertrand Cosson
- Université Paris Cité, CNRS, Epigenetics and Cell Fate, UMR7216, 75013 Paris, France
| | - Slimane Ait-Si-Ali
- Université Paris Cité, CNRS, Epigenetics and Cell Fate, UMR7216, 75013 Paris, France
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2
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Bulfoni M, Bouyioukos C, Zakaria A, Nigon F, Rapone R, Del Maestro L, Ait-Si-Ali S, Scharfmann R, Cosson B. Glucose controls co-translation of structurally related mRNAs via the mTOR and eIF2 pathways in human pancreatic beta cells. Front Endocrinol (Lausanne) 2022; 13:949097. [PMID: 35992129 PMCID: PMC9388909 DOI: 10.3389/fendo.2022.949097] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 05/20/2022] [Accepted: 07/11/2022] [Indexed: 11/13/2022] Open
Abstract
Pancreatic beta cell response to glucose is critical for the maintenance of normoglycemia. A strong transcriptional response was classically described in rodent models but, interestingly, not in human cells. In this study, we exposed human pancreatic beta cells to an increased concentration of glucose and analysed at a global level the mRNAs steady state levels and their translationalability. Polysome profiling analysis showed an early acute increase in protein synthesis and a specific translation regulation of more than 400 mRNAs, independently of their transcriptional regulation. We clustered the co-regulated mRNAs according to their behaviour in translation in response to glucose and discovered common structural and sequence mRNA features. Among them mTOR- and eIF2-sensitive elements have a predominant role to increase mostly the translation of mRNAs encoding for proteins of the translational machinery. Furthermore, we show that mTOR and eIF2α pathways are independently regulated in response to glucose, participating to a translational reshaping to adapt beta cell metabolism. The early acute increase in the translation machinery components prepare the beta cell for further protein demand due to glucose-mediated metabolism changes.
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Affiliation(s)
- Manuel Bulfoni
- Université Paris Cité, CNRS, Epigenetics and Cell Fate, Paris, France
| | - Costas Bouyioukos
- Université Paris Cité, CNRS, Epigenetics and Cell Fate, Paris, France
| | - Albatoul Zakaria
- Université Paris Cité, Institut Cochin, INSERM, CNRS, Paris, France
| | - Fabienne Nigon
- Université Paris Cité, CNRS, Epigenetics and Cell Fate, Paris, France
| | - Roberta Rapone
- Université Paris Cité, CNRS, Epigenetics and Cell Fate, Paris, France
| | | | | | | | - Bertrand Cosson
- Université Paris Cité, CNRS, Epigenetics and Cell Fate, Paris, France
- *Correspondence: Bertrand Cosson,
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3
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Zakaria A, Berthault C, Cosson B, Jung V, Guerrera IC, Rachdi L, Scharfmann R. Glucose treatment of human pancreatic β-cells enhances translation of mRNAs involved in energetics and insulin secretion. J Biol Chem 2021; 297:100839. [PMID: 34051232 PMCID: PMC8253965 DOI: 10.1016/j.jbc.2021.100839] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2020] [Revised: 05/17/2021] [Accepted: 05/25/2021] [Indexed: 12/30/2022] Open
Abstract
Glucose-mediated signaling regulates the expression of a limited number of genes in human pancreatic β-cells at the transcriptional level. However, it is unclear whether glucose plays a role in posttranscriptional RNA processing or translational control of gene expression. Here, we asked whether glucose affects posttranscriptional steps and regulates protein synthesis in human β-cell lines. We first showed the involvement of the mTOR pathway in glucose-related signaling. We also used the surface sensing of translation technique, based on puromycin incorporation into newly translated proteins, to demonstrate that glucose treatment increased protein translation. Among the list of glucose-induced proteins, we identified the proconvertase PCSK1, an enzyme involved in the proteolytic conversion of proinsulin to insulin, whose translation was induced within minutes following glucose treatment. We finally performed global proteomic analysis by mass spectrometry to characterize newly translated proteins upon glucose treatment. We found enrichment in proteins involved in translation, glycolysis, TCA metabolism, and insulin secretion. Taken together, our study demonstrates that, although glucose minorly affects gene transcription in human β-cells, it plays a major role at the translational level.
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Affiliation(s)
- Albatoul Zakaria
- Institut Cochin, INSERM U1016, CNRS UMR 8104, Université de Paris, Paris, France
| | - Claire Berthault
- Institut Cochin, INSERM U1016, CNRS UMR 8104, Université de Paris, Paris, France
| | - Bertrand Cosson
- Epigenetics and Cell Fate Center, CNRS UMR 7216, Université de Paris, Paris, France
| | - Vincent Jung
- Plateforme protéomique Necker, INSERM US24/CNRS UMS3633, Université de Paris, Structure Fédérative de Recherche Necker, Paris, France
| | - Ida Chiara Guerrera
- Plateforme protéomique Necker, INSERM US24/CNRS UMS3633, Université de Paris, Structure Fédérative de Recherche Necker, Paris, France
| | - Latif Rachdi
- Institut Cochin, INSERM U1016, CNRS UMR 8104, Université de Paris, Paris, France.
| | - Raphael Scharfmann
- Institut Cochin, INSERM U1016, CNRS UMR 8104, Université de Paris, Paris, France.
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4
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Boussaid I, Le Goff S, Floquet C, Gautier EF, Raimbault A, Viailly PJ, Al Dulaimi D, Burroni B, Dusanter-Fourt I, Hatin I, Mayeux P, Cosson B, Fontenay M. Integrated analyses of translatome and proteome identify the rules of translation selectivity in RPS14-deficient cells. Haematologica 2021; 106:746-758. [PMID: 32327500 PMCID: PMC7927886 DOI: 10.3324/haematol.2019.239970] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/07/2019] [Indexed: 12/24/2022] Open
Abstract
In ribosomopathies, the Diamond-Blackfan anemia (DBA) or 5q- syndrome, ribosomal protein (RP) genes are affected by mutation or deletion, resulting in bone marrow erythroid hypoplasia. Unbalanced production of ribosomal subunits leading to a limited ribosome cellular content regulates translation at the expense of the master erythroid transcription factor GATA1. In RPS14-deficient cells mimicking 5q- syndrome erythroid defects, we show that the transcript length, codon bias of the coding sequence (CDS) and 3’UTR (untranslated region) structure are the key determinants of translation. In these cells, short transcripts with a structured 3’UTR and high codon adaptation index (CAI) showed a decreased translation efficiency. Quantitative analysis of the whole proteome confirmed that the post-transcriptional changes depended on the transcript characteristics that governed the translation efficiency in conditions of low ribosome availability. In addition, proteins involved in normal erythroid differentiation share most determinants of translation selectivity. Our findings thus indicate that impaired erythroid maturation due to 5q- syndrome may proceed from a translational selectivity at the expense of the erythroid differentiation program, and suggest that an interplay between the CDS and UTR may regulate mRNA translation.
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Affiliation(s)
- Ismael Boussaid
- Université de Paris, Institut Cochin, CNRS UMR 8104, INSERM U1016, Paris
| | - Salomé Le Goff
- Université de Paris, Institut Cochin, CNRS UMR 8104, INSERM U1016, Paris,Laboratoire d’Excellence du Globule Rouge GR-Ex, Université de Paris, Paris
| | - Célia Floquet
- Université de Paris, Institut Cochin, CNRS UMR 8104, INSERM U1016, Paris
| | - Emilie-Fleur Gautier
- Université de Paris, Institut Cochin, CNRS UMR 8104, INSERM U1016, Paris,Centre-Université de Paris Cochin, Service de Pathologie, Paris, France
| | - Anna Raimbault
- Université de Paris, Institut Cochin, CNRS UMR 8104, INSERM U1016, Paris
| | - Pierre-Julien Viailly
- Centre Henri-Becquerel, Institut de Recherche et d’Innovation Biomedicale de Haute Normandie, INSERM U1245, Rouen
| | - Dina Al Dulaimi
- Université de Paris, Institut Cochin, CNRS UMR 8104, INSERM U1016, Paris
| | - Barbara Burroni
- Assistance Publique-Hôpitaux de Paris, Centre-Université de Paris - Cochin, Service de Pathologie, Paris
| | | | - Isabelle Hatin
- Institute for Integrative Biology of the Cell (I2BC), CEA, CNRS, Université de Paris-Sud, Université Paris-Saclay, Gif-sur-Yvette Cedex
| | - Patrick Mayeux
- Université de Paris, Institut Cochin, CNRS UMR 8104, INSERM U1016, Paris,Laboratoire d’Excellence du Globule Rouge GR-Ex, Université de Paris, Paris,Centre-Université de Paris Cochin, Service de Pathologie, Paris, France
| | - Bertrand Cosson
- Université de Paris, Epigenetics and Cell Fate, CNRS UMR 7216, Paris
| | - Michaela Fontenay
- Université de Paris, Institut Cochin, CNRS UMR 8104, INSERM U1016, Paris,Laboratoire d’Excellence du Globule Rouge GR-Ex, Université de Paris, Paris,Centre-Université de Paris Cochin, Service de Pathologie, Paris, France.,Centre Henri-Becquerel, Institut de Recherche et d’Innovation Biomedicale de Haute Normandie, INSERM U1245, Rouen,Assistance Publique- Hôpitaux de Paris, Centre-Université de Paris - Hôpital Cochin, Service d’Hématologie Biologique, Paris, France
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5
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Penrad-Mobayed M, Perrin C, Herman L, Todeschini AL, Nigon F, Cosson B, Caburet S, Veitia RA. Conventional and unconventional interactions of the transcription factor FOXL2 uncovered by a proteome-wide analysis. FASEB J 2019; 34:571-587. [PMID: 31914586 DOI: 10.1096/fj.201901573r] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/24/2019] [Revised: 09/11/2019] [Accepted: 10/08/2019] [Indexed: 12/19/2022]
Abstract
Beyond the study of its transcriptional target genes, the identification of the various interactors of a transcription factor (TF) is crucial to understand its diverse cellular roles. We focused on FOXL2, a winged-helix forkhead TF important for ovarian development and maintenance. FOXL2 has been implicated in diverse cellular processes, including apoptosis, the control of cell cycle or the regulation of steroid hormone synthesis. To reliably identify partners of endogenous FOXL2, we performed a proteome-wide analysis using co-immunoprecipitation in the murine granulosa cell-derived AT29c and the pituitary-derived alpha-T3 cell lines, using three antibodies targeting different parts of the protein. Following a stringent selection of mass spectrometry data on the basis of identification reliability and protein enrichment, we identified a core set of 255 partners common to both cell lines. Their analysis showed that we could co-precipitate several complexes involved in mRNA processing, chromatin remodeling and DNA replication and repair. We further validated (direct and/or indirect) interactions with selected partners, suggesting an unexpected role for FOXL2 in those processes. Overall, this comprehensive analysis of the endogenous FOXL2 interactome sheds light on its numerous and diverse interactors and unconventional cellular roles.
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Affiliation(s)
- May Penrad-Mobayed
- Institut Jacques Monod, CNRS UMR7592, Université de Paris, Paris, France
| | - Caroline Perrin
- Institut Jacques Monod, CNRS UMR7592, Université de Paris, Paris, France
| | - Laetitia Herman
- Institut Jacques Monod, CNRS UMR7592, Université de Paris, Paris, France
| | | | - Fabienne Nigon
- Epigenetics and Cell Fate, CNRS UMR7216, Université de Paris, Paris, France
| | - Bertrand Cosson
- Epigenetics and Cell Fate, CNRS UMR7216, Université de Paris, Paris, France
| | - Sandrine Caburet
- Institut Jacques Monod, CNRS UMR7592, Université de Paris, Paris, France
| | - Reiner A Veitia
- Institut Jacques Monod, CNRS UMR7592, Université de Paris, Paris, France
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6
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Middleton R, Gao D, Thomas A, Singh B, Au A, Wong JJL, Bomane A, Cosson B, Eyras E, Rasko JEJ, Ritchie W. IRFinder: assessing the impact of intron retention on mammalian gene expression. Genome Biol 2017; 18:51. [PMID: 28298237 PMCID: PMC5353968 DOI: 10.1186/s13059-017-1184-4] [Citation(s) in RCA: 140] [Impact Index Per Article: 20.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/08/2016] [Accepted: 02/27/2017] [Indexed: 01/05/2023] Open
Abstract
Intron retention (IR) occurs when an intron is transcribed into pre-mRNA and remains in the final mRNA. We have developed a program and database called IRFinder to accurately detect IR from mRNA sequencing data. Analysis of 2573 samples showed that IR occurs in all tissues analyzed, affects over 80% of all coding genes and is associated with cell differentiation and the cell cycle. Frequently retained introns are enriched for specific RNA binding protein sites and are often retained in clusters in the same gene. IR is associated with lower protein levels and intron-retaining transcripts that escape nonsense-mediated decay are not actively translated.
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Affiliation(s)
- Robert Middleton
- Bioinformatics Laboratory, Centenary Institute, Camperdown, 2050, Australia
| | - Dadi Gao
- Bioinformatics Laboratory, Centenary Institute, Camperdown, 2050, Australia.,Molecular Neurogenetics Unit, Center for Human Genetic Research, Massachusetts General Hospital, Boston, MA, USA.,Boston & Harvard Medical School, Boston, MA, USA.,Gene & Stem Cell Therapy Program, Centenary Institute, Camperdown, 2050, Australia
| | | | - Babita Singh
- Pompeu Fabra University, UPF, Dr. Aiguader 88, E08003, Barcelona, Spain
| | - Amy Au
- Gene & Stem Cell Therapy Program, Centenary Institute, Camperdown, 2050, Australia.,Sydney Medical School, University of Sydney, Sydney, NSW, 2006, Australia
| | - Justin J-L Wong
- Gene & Stem Cell Therapy Program, Centenary Institute, Camperdown, 2050, Australia.,Sydney Medical School, University of Sydney, Sydney, NSW, 2006, Australia.,Gene Regulation in Cancer Laboratory, Centenary Institute, University of Sydney, Camperdown, 2050, Australia
| | - Alexandra Bomane
- Université Paris Diderot, Sorbonne Paris Cité, Epigenetics and Cell Fate, UMR7216, CNRS, F-75013, Paris, France
| | - Bertrand Cosson
- Université Paris Diderot, Sorbonne Paris Cité, Epigenetics and Cell Fate, UMR7216, CNRS, F-75013, Paris, France
| | - Eduardo Eyras
- Pompeu Fabra University, UPF, Dr. Aiguader 88, E08003, Barcelona, Spain.,Catalan Institution for Research and Advanced Studies, ICREA, Passeig Lluís Companys 23, E08010, Barcelona, Spain
| | - John E J Rasko
- Gene & Stem Cell Therapy Program, Centenary Institute, Camperdown, 2050, Australia.,Sydney Medical School, University of Sydney, Sydney, NSW, 2006, Australia.,Cell and Molecular Therapies, Royal Prince Alfred Hospital, Camperdown, 2050, Australia
| | - William Ritchie
- Bioinformatics Laboratory, Centenary Institute, Camperdown, 2050, Australia. .,CNRS, UPR 1142, Montpellier, 34094, France. .,CNRS, UMR 5203, Montpellier, 34094, France.
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7
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Jiblaoui A, Barbeau J, Vivès T, Cormier P, Glippa V, Cosson B, Benvegnu T. Folate-conjugated stealth archaeosomes for the targeted delivery of novel antitumoral peptides. RSC Adv 2016. [DOI: 10.1039/c6ra15713k] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022] Open
Abstract
In this work, novel archaeosomes based on Egg-PC and a mixture of PEGylated archaeal tetraether lipids were investigated as nanocarriers forin vitrodelivery of an original anticancer peptide.
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Affiliation(s)
- Ahmad Jiblaoui
- Ecole Nationale Supérieure de Chimie de Rennes
- UMR CNRS 6226
- Equipe Chimie Organique et Supramoléculaire
- 35708 Rennes Cedex 7
- France
| | - Julie Barbeau
- Ecole Nationale Supérieure de Chimie de Rennes
- UMR CNRS 6226
- Equipe Chimie Organique et Supramoléculaire
- 35708 Rennes Cedex 7
- France
| | - Thomas Vivès
- Ecole Nationale Supérieure de Chimie de Rennes
- UMR CNRS 6226
- Equipe Chimie Organique et Supramoléculaire
- 35708 Rennes Cedex 7
- France
| | - Patrick Cormier
- Sorbonne Universités
- UPMC Univ Paris 06
- UMR CNRS 8227
- Integrative Biology of Marine Models
- Translation Cell Cycle and Development
| | - Virginie Glippa
- Sorbonne Universités
- UPMC Univ Paris 06
- UMR CNRS 8227
- Integrative Biology of Marine Models
- Translation Cell Cycle and Development
| | - Bertrand Cosson
- Sorbonne Universités
- UPMC Univ Paris 06
- UMR CNRS 8227
- Integrative Biology of Marine Models
- Translation Cell Cycle and Development
| | - Thierry Benvegnu
- Ecole Nationale Supérieure de Chimie de Rennes
- UMR CNRS 6226
- Equipe Chimie Organique et Supramoléculaire
- 35708 Rennes Cedex 7
- France
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8
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Gosselin P, Martineau Y, Morales J, Czjzek M, Glippa V, Gauffeny I, Morin E, Le Corguillé G, Pyronnet S, Cormier P, Cosson B. Tracking a refined eIF4E-binding motif reveals Angel1 as a new partner of eIF4E. Nucleic Acids Res 2013; 41:7783-92. [PMID: 23814182 PMCID: PMC3763552 DOI: 10.1093/nar/gkt569] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
The initiation factor 4E (eIF4E) is implicated in most of the crucial steps of the mRNA life cycle and is recognized as a pivotal protein in gene regulation. Many of these roles are mediated by its interaction with specific proteins generally known as eIF4E-interacting partners (4E-IPs), such as eIF4G and 4E-BP. To screen for new 4E-IPs, we developed a novel approach based on structural, in silico and biochemical analyses. We identified the protein Angel1, a member of the CCR4 deadenylase family. Immunoprecipitation experiments provided evidence that Angel1 is able to interact in vitro and in vivo with eIF4E. Point mutation variants of Angel1 demonstrated that the interaction of Angel1 with eIF4E is mediated through a consensus eIF4E-binding motif. Immunofluorescence and cell fractionation experiments showed that Angel1 is confined to the endoplasmic reticulum and Golgi apparatus, where it partially co-localizes with eIF4E and eIF4G, but not with 4E-BP. Furthermore, manipulating Angel1 levels in living cells had no effect on global translation rates, suggesting that the protein has a more specific function. Taken together, our results illustrate that we developed a powerful method for identifying new eIF4E partners and open new perspectives for understanding eIF4E-specific regulation.
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Affiliation(s)
- Pauline Gosselin
- UPMC Univ Paris 06, UMR 7150, Mer et Santé, Station Biologique, F-29680 Roscoff, France, CNRS, UMR 7150, Mer et Santé, Station Biologique, F-29680 Roscoff, France. Université Européenne de Bretagne, Bretagne, Roscoff, France, INSERM, UMR 1037, Centre de Recherche en Cancérologie de Toulouse, Toulouse 31432, France, UPMC Univ Paris 06, UMR 7139, Végétaux Marins et Biomolécules, Station Biologique, F-29680 Roscoff, France, CNRS, UMR 7139, Végétaux Marins et Biomolécules, Station Biologique, F-29680 Roscoff, France, UPMC Univ Paris 06, FR2424, ABiMS, Station Biologique, F-29680 Roscoff, France and CNRS, FR2424, ABiMS, Station Biologique, F-29680 Roscoff, France
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9
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Cosson B, Chevalier L, Yvonnet J. Optimization of the Thickness of PET Bottles during Stretch Blow Molding by Using a Mesh-free (Numerical) Method. INT POLYM PROC 2013. [DOI: 10.3139/217.2215] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
Abstract
Abstract
The stretch-blow molding process of polyethylene terephthalate (PET) bottles generates some important modifications in the mechanical properties of the material. Considering, the process temperature (T > Tg) that is usually used, the material exhibits a very high viscosity and involves a strain hardening effect associated with the microstructure evolution. An anisotropic viscoplastic model coupled with induced properties, identified from experimental results of uniaxial and biaxial tensile tests previously published by Chevalier and Marco (2006), is presented in a first part of the paper. Secondly, we perform a numerical simulation to simulate the free inflation of a preform under an internal pressure with different parameters. Because the final strains are up to 300 to 400%, it generates important distortion of node distribution and we chose to use the mesh-free Constrained Natural Elements Method (C-NEM) for numerical simulation. The final goal is to use these simulations in order to fit the best parameter set leading to a quasi-homogeneous distribution of the thickness along the bottle. Homogeneous thickness implies homogeneous biaxial stretching and more uniform induced properties for the final bottle and this is an important industrial goal.
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Affiliation(s)
- B. Cosson
- Université Paris-Est, Laboratoire Modelisation et Simulation Multi Echelle, Marne-la-Vallée, France
| | - L. Chevalier
- Université Paris-Est, Laboratoire Modelisation et Simulation Multi Echelle, Marne-la-Vallée, France
| | - J. Yvonnet
- Université Paris-Est, Laboratoire Modelisation et Simulation Multi Echelle, Marne-la-Vallée, France
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10
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Cosson B, Braun F, Paillard L, Blackshear P, Beverley Osborne H. Identification of a novel Xenopus laevis poly (A) binding protein. Biol Cell 2012; 96:519-27. [PMID: 15380618 DOI: 10.1016/j.biolcel.2004.04.006] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/02/2004] [Accepted: 04/29/2004] [Indexed: 11/28/2022]
Abstract
Poly (A) binding proteins are intimately implicated in controlling a number of events in mRNA metabolism from nuclear polyadenylation to cytoplasmic translation and stability. The known poly(A) binding proteins can be divided into three distinct structural groups (prototypes PABP1, PABPN1/PABP2 and Nab2p) and two functional families, showing that similar functions can be accomplished by differing structural units. This has prompted us to perform a screen for novel poly(A) binding proteins using Xenopus laevis. A novel poly(A) binding protein of 32 kDa (p32) was identified. Sequence analysis showed that p32 has about 50% identity to the known nuclear poly(A) binding proteins (PABPN1) but is more closely related to a group of mammalian proteins of unknown function. The expression of Xenopus laevis ePABP2 is restricted to early embryos. Accordingly, we propose that p32 is the founder member of a novel class of poly(A) binding proteins named ePABP2.
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Affiliation(s)
- Bertrand Cosson
- UMR6061 CNRS--Génétique et Développement, Université de Rennes 1, Faculté de Médecine, 2 avenue Professeur Leon Bernard, CS 34317, 35043 Rennes cedex, France.
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11
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Gosselin P, Oulhen N, Jam M, Ronzca J, Cormier P, Czjzek M, Cosson B. The translational repressor 4E-BP called to order by eIF4E: new structural insights by SAXS. Nucleic Acids Res 2010; 39:3496-503. [PMID: 21183464 PMCID: PMC3082885 DOI: 10.1093/nar/gkq1306] [Citation(s) in RCA: 42] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023] Open
Abstract
eIF4E binding protein (4E-BP) inhibits translation of capped mRNA by binding to the initiation factor eIF4E and is known to be mostly or completely unstructured in both free and bound states. Using small angle X-ray scattering (SAXS), we report here the analysis of 4E-BP structure in solution, which reveals that while 4E-BP is intrinsically disordered in the free state, it undergoes a dramatic compaction in the bound state. Our results demonstrate that 4E-BP and eIF4E form a ‘fuzzy complex’, challenging current visions of eIF4E/4E-BP complex regulation.
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Affiliation(s)
- Pauline Gosselin
- UPMC Univ Paris 06, UMR 7150, Mer et Santé, Equipe Traduction Cycle Cellulaire et Développement, Station Biologique de Roscoff, 29680 Roscoff, France.
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12
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Keryer-Bibens C, Legagneux V, Namanda-Vanderbeken A, Cosson B, Paillard L, Poncet D, Osborne HB. The rotaviral NSP3 protein stimulates translation of polyadenylated target mRNAs independently of its RNA-binding domain. Biochem Biophys Res Commun 2009; 390:302-6. [PMID: 19800313 DOI: 10.1016/j.bbrc.2009.09.115] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/08/2009] [Accepted: 09/24/2009] [Indexed: 11/26/2022]
Abstract
The non-structural protein 3 (NSP3) of rotaviruses is an RNA-binding protein that specifically recognises a 4 nucleotide sequence at the 3' extremity of the non-polyadenylated viral mRNAs. NSP3 also has a high affinity for eIF4G. These two functions are clearly delimited in separate domains the structures of which have been determined. They are joined by a central domain implicated in the dimerisation of the full length protein. The bridging function of NSP3 between the 3' end of the viral mRNA and eIF4G has been proposed to enhance the synthesis of viral proteins. However, this role has been questioned as knock-down of NSP3 did not impair viral protein synthesis. We show here using a MS2/MS2-CP tethering assay that a C-terminal fragment of NSP3 containing the eIF4G binding domain and the dimerisation domain can increase the expression of a protein encoded by a target reporter mRNA in HEK 293 cells. The amount of reporter mRNA in the cells is not significantly affected by the presence of the NSP3 derived fusion protein showing that the enhanced protein expression is due to increased translation. These results show that NSP3 can act as a translational enhancer even on a polyadenylated mRNA that should be a substrate for PABP1.
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Affiliation(s)
- Cécile Keryer-Bibens
- Université de Rennes 1, IFR 140, Institut de Génétique et Développement de Rennes, 35000 Rennes, France.
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Oulhen N, Boulben S, Bidinosti M, Morales J, Cormier P, Cosson B. A variant mimicking hyperphosphorylated 4E-BP inhibits protein synthesis in a sea urchin cell-free, cap-dependent translation system. PLoS One 2009; 4:e5070. [PMID: 19333389 PMCID: PMC2659438 DOI: 10.1371/journal.pone.0005070] [Citation(s) in RCA: 30] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/07/2008] [Accepted: 03/03/2009] [Indexed: 12/03/2022] Open
Abstract
Background 4E-BP is a translational inhibitor that binds to eIF4E to repress cap-dependent translation initiation. This critical protein:protein interaction is regulated by the phosphorylation of 4E-BP. Hypophosphorylated 4E-BP binds to eIF4E and inhibits cap-dependent translation, whereas hyperphosphorylated forms do not. While three 4E-BP proteins exist in mammals, only one gene encoding for 4E-BP is present in the sea urchin genome. The protein product has a highly conserved core domain containing the eIF4E-binding domain motif (YxxxxLΦ) and four of the regulatory phosphorylation sites. Methodology/Principal Findings Using a sea urchin cell-free cap-dependent translation system prepared from fertilized eggs, we provide the first direct evidence that the sea urchin 4E-BP inhibits cap-dependent translation. We show here that a sea urchin 4E-BP variant, mimicking phosphorylation on four core residues required to abrogate binding to eIF4E, surprisingly maintains physical association to eIF4E and inhibits protein synthesis. Conclusions/Significance Here, we examine the involvement of the evolutionarily conserved core domain and phosphorylation sites of sea urchin 4E-BP in the regulation of eIF4E-binding. These studies primarily demonstrate the conserved activity of the 4E-BP translational repressor and the importance of the eIF4E-binding domain in sea urchin. We also show that a variant mimicking hyperphosphorylation of the four regulatory phosphorylation sites common to sea urchin and human 4E-BP is not sufficient for release from eIF4E and translation promotion. Therefore, our results suggest that there are additional mechanisms to that of phosphorylation at the four critical sites of 4E-BP that are required to disrupt binding to eIF4E.
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Affiliation(s)
- Nathalie Oulhen
- UPMC Univ Paris 06, UMR 7150, Equipe Traduction Cycle Cellulaire et Développement, Station Biologique de Roscoff, Roscoff, France
- CNRS, UMR 7150, Station Biologique de Roscoff, Roscoff, France
- Université Européenne de Bretagne, Bretagne, France
| | - Sandrine Boulben
- UPMC Univ Paris 06, UMR 7150, Equipe Traduction Cycle Cellulaire et Développement, Station Biologique de Roscoff, Roscoff, France
- CNRS, UMR 7150, Station Biologique de Roscoff, Roscoff, France
- Université Européenne de Bretagne, Bretagne, France
| | - Michael Bidinosti
- Department of Biochemistry and Rosalind and Morris Goodman Cancer Centre, McGill University, Montreal, Quebec, Canada
| | - Julia Morales
- UPMC Univ Paris 06, UMR 7150, Equipe Traduction Cycle Cellulaire et Développement, Station Biologique de Roscoff, Roscoff, France
- CNRS, UMR 7150, Station Biologique de Roscoff, Roscoff, France
- Université Européenne de Bretagne, Bretagne, France
| | - Patrick Cormier
- UPMC Univ Paris 06, UMR 7150, Equipe Traduction Cycle Cellulaire et Développement, Station Biologique de Roscoff, Roscoff, France
- CNRS, UMR 7150, Station Biologique de Roscoff, Roscoff, France
- Université Européenne de Bretagne, Bretagne, France
| | - Bertrand Cosson
- UPMC Univ Paris 06, UMR 7150, Equipe Traduction Cycle Cellulaire et Développement, Station Biologique de Roscoff, Roscoff, France
- CNRS, UMR 7150, Station Biologique de Roscoff, Roscoff, France
- Université Européenne de Bretagne, Bretagne, France
- * E-mail:
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14
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Saad H, Bellé R, Morales J, Cosson B, Mulner-Lorillon O, Berthou C, Cormier P. [Initiation factors eIF4: from sea urchin embryonic development to chronic lymphocytic leukemia]. ACTA ACUST UNITED AC 2008; 201:307-15. [PMID: 18157083 DOI: 10.1051/jbio:2007029] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022]
Abstract
mRNA translation is now recognized as a important regulatory step for gene expression in different physiological and pathophysiological processes including cell proliferation and apoptosis. B-cell chronic lymphocytic leukemia (B-CLL) is characterized by the accumulation of resting lymphocytes and defective apoptosis. The mRNA cap-binding protein eIF4E (eukaryotic Initiation Factor 4E) and its repressor 4E-BP (eIF4E Binding protein) are crucial translational regulators that have been involved in survival and apoptosis processes of cells. We have shown that the release of eIF4E from its translational repressor 4E-BP is an important event for the first mitotic division triggered by fertilization and that the degradation of 4E-BP is a new means to regulate 4E-BP function that has to be analyzed in other physiological and physiopathological processes. In this chapter, we describe recent advances illustrating the importance of eIF4E and 4E-BP in cancer processes, suggesting that these actors can be targeted for potential therapy against cancer in general and LLC in particular.
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Affiliation(s)
- Hussam Saad
- Centre National de la Recherche Scientifique, UMR 7150 Mer & Santé, France.
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15
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Bellé R, Le Bouffant R, Morales J, Cosson B, Cormier P, Mulner-Lorillon O. L'embryon d'oursin, le point de surveillance de l'ADN endommagé de la division cellulaire et les mécanismes à l'origine de la cancérisation. ACTA ACUST UNITED AC 2008; 201:317-27. [DOI: 10.1051/jbio:2007030] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022]
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16
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Oulhen N, Morales J, Cosson B, Mulner-Lorillon O, Bellé R, Cormier P. [Gene expression regulation at the translational level: contribution of marine organisms]. ACTA ACUST UNITED AC 2007; 201:297-306. [PMID: 18157082 DOI: 10.1051/jbio:2007028] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022]
Abstract
Gene expression regulation is crucial for organism survival. Each step has to be regulated, from the gene to the protein. mRNA can be stored in the cell without any direct translation. This process is used by the cell to control protein synthesis rapidly at the right place, at the right time. Protein synthesis costs a lot of energy for the cell, so that a precise control of this process is required. Translation initiation represents an important step to regulate gene expression. Many factors that can bind mRNA and recruit different partners are involved in the inhibition or stimulation of protein synthesis. Oceans contain an important diversity of organisms that are used as important models to analyse gene expression at the translational level. These are useful to study translational control in different physiological processes for instance cell cycle (meiosis during meiotic maturation of starfish oocytes, mitosis following fertilization of sea urchin eggs) or to understand nervous system mechanisms (aplysia). All these studies will help finding novel actors involved in translational control and will thus be useful to discover new targets for therapeutic treatments against human diseases.
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Affiliation(s)
- Nathalie Oulhen
- Centre National de la Recherche Scientifique, UMR 7150 Mer et Santé, France.
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17
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Cosson B, Gautier-Courteille C, Maniey D, Aït-Ahmed O, Lesimple M, Osborne HB, Paillard L. Oligomerization of EDEN-BP is required for specific mRNA deadenylation and binding. Biol Cell 2007; 98:653-65. [PMID: 16836486 DOI: 10.1042/bc20060054] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
Abstract
BACKGROUND INFORMATION mRNA deadenylation [shortening of the poly(A) tail] is often triggered by specific sequence elements present within mRNA 3' untranslated regions and generally causes rapid degradation of the mRNA. In vertebrates, many of these deadenylation elements are called AREs (AU-rich elements). The EDEN (embryo deadenylation element) sequence is a Xenopus class III ARE. EDEN acts by binding a specific factor, EDEN-BP (EDEN-binding protein), which in turn stimulates deadenylation. RESULTS We show here that EDEN-BP is able to oligomerize. A 27-amino-acid region of EDEN-BP was identified as a key domain for oligomerization. A mutant of EDEN-BP lacking this region was unable to oligomerize, and a peptide corresponding to this region competitively inhibited the oligomerization of full-length EDEN-BP. Impairing oligomerization by either of these two methods specifically abolished EDEN-dependent deadenylation. Furthermore, impairing oligomerization inhibited the binding of EDEN-BP to its target RNA, demonstrating a strong coupling between EDEN-BP oligomerization and RNA binding. CONCLUSIONS These data, showing that the oligomerization of EDEN-BP is required for binding of the protein on its target RNA and for EDEN-dependent deadenylation in Xenopus embryos, will be important for the identification of cofactors required for the deadenylation process.
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Affiliation(s)
- Bertrand Cosson
- CNRS UMR 6061, IFR 140, Université de Rennes 1, Faculté de Médecine, 2 Avenue Léon Bernard, 35043 Rennes Cedex, France
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18
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Oulhen N, Salaün P, Cosson B, Cormier P, Morales J. After fertilization of sea urchin eggs, eIF4G is post-translationally modified and associated with the cap-binding protein eIF4E. J Cell Sci 2007; 120:425-34. [PMID: 17213333 DOI: 10.1242/jcs.03339] [Citation(s) in RCA: 16] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Release of eukaryotic initiation factor 4E (eIF4E) from its translational repressor eIF4E-binding protein (4E-BP) is a crucial event for the first mitotic division following fertilization of sea urchin eggs. Finding partners of eIF4E following fertilization is crucial to understand how eIF4E functions during this physiological process. The isolation and characterization of cDNA encoding Sphaerechinus granularis eIF4G (SgIF4G) are reported. mRNA of SgIF4G is present as a single 8.5-kb transcript in unfertilized eggs, suggesting that only one ortholog exists in echinoderms. The longest open reading frame predicts a sequence of 5235 nucleotides encoding a deduced polypeptide of 1745 amino acids with a predicted molecular mass of 192 kDa. Among highly conserved domains, SgIF4G protein possesses motifs that correspond to the poly(A) binding protein and eIF4E protein-binding sites. A specific polyclonal antibody was produced and used to characterize the SgIF4G protein in unfertilized and fertilized eggs by SDS-PAGE and western blotting. Multiple differentially migrating bands representing isoforms of sea urchin eIF4G are present in unfertilized eggs. Fertilization triggers modifications of the SgIF4G isoforms and rapid formation of the SgIF4G-eIF4E complex. Whereas rapamycin inhibits the formation of the SgIF4G-eIF4E complex, modification of these SgIF4G isoforms occurs independently from the rapamycin-sensitive pathway. Microinjection of a peptide corresponding to the eIF4E-binding site derived from the sequence of SgIF4G into unfertilized eggs affects the first mitotic division of sea urchin embryos. Association of SgIF4G with eIF4E is a crucial event for the onset of the first mitotic division following fertilization, suggesting that cap-dependent translation is highly regulated during this process. This hypothesis is strengthened by the evidence that microinjection of the cap analog m(7)GDP into unfertilized eggs inhibits the first mitotic division.
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Affiliation(s)
- Nathalie Oulhen
- Université Pierre et Marie Curie-Paris6, UMR 7150, Equipe Cycle Cellulaire et Développement and CNRS, UMR 7150, Station Biologique de Roscoff, 29682 Roscoff CEDEX, France
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19
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Morales J, Mulner-Lorillon O, Cosson B, Morin E, Bellé R, Bradham CA, Beane WS, Cormier P. Translational control genes in the sea urchin genome. Dev Biol 2006; 300:293-307. [PMID: 16959243 DOI: 10.1016/j.ydbio.2006.07.036] [Citation(s) in RCA: 25] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/29/2006] [Revised: 07/25/2006] [Accepted: 07/27/2006] [Indexed: 10/24/2022]
Abstract
Sea urchin eggs and early cleavage stage embryos provide an example of regulated gene expression at the level of translation. The availability of the sea urchin genome offers the opportunity to investigate the "translational control" toolkit of this model system. The annotation of the genome reveals that most of the factors implicated in translational control are encoded by nonredundant genes in echinoderm, an advantage for future functional studies. In this paper, we focus on translation factors that have been shown or suggested to play crucial role in cell cycle and development of sea urchin embryos. Addressing the cap-binding translational control, three closely related eIF4E genes (class I, II, III) are present, whereas its repressor 4E-BP and its activator eIF4G are both encoded by one gene. Analysis of the class III eIF4E proteins in various phyla shows an echinoderm-specific amino acid substitution. Furthermore, an interaction site between eIF4G and poly(A)-binding protein is uncovered in the sea urchin eIF4G proteins and is conserved in metazoan evolution. In silico screening of the sea urchin genome has uncovered potential new regulators of eIF4E sharing the common eIF4E recognition motif. Taking together, these data provide new insights regarding the strong requirement of cap-dependent translation following fertilization. The genome analysis gives insights on the complexity of eEF1B structure and motifs of functional relevance, involved in the translational control of gene expression at the level of elongation. Finally, because deregulation of translation process can lead to diseases and tumor formation in humans, the sea urchin orthologs of human genes implicated in human diseases and signaling pathways regulating translation were also discussed.
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Affiliation(s)
- Julia Morales
- Equipe Cycle Cellulaire et Développement, UMR 7150 CNRS/UPMC, Station Biologique 29680 Roscoff, France.
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20
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Sagliocco F, Laloo B, Cosson B, Laborde L, Castroviejo M, Rosenbaum J, Ripoche J, Grosset C. The ARE-associated factor AUF1 binds poly(A) in vitro in competition with PABP. Biochem J 2006; 400:337-47. [PMID: 16834569 PMCID: PMC1652824 DOI: 10.1042/bj20060328] [Citation(s) in RCA: 17] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
Abstract
The ARE (AU-rich element) is a post-transcriptional element controlling both mRNA turnover and translation initiation by primarily inducing poly(A) tail shortening. The mechanisms by which the ARE-associated proteins induce deadenylation are still obscure. One possibility among others would be that an ARE-ARE-BP (ARE-binding protein) complex intervenes in the PABP [poly(A)-binding protein]-poly(A) tail association and facilitates poly(A) tail accessibility to deadenylases. Here, we show by several experimental approaches that AUF1 (AU-rich element RNA-binding protein 1)/hnRNP (heterogeneous nuclear ribonucleoprotein) D, an mRNA-destabilizing ARE-BP, can bind poly(A) sequence in vitro. First, endogenous AUF1 proteins from HeLa cells specifically bound poly(A), independently of PABP. Secondly, using polyadenylated RNA probes, we showed that (i) the four recombinant AUF1 isoforms bind poly(A) as efficiently as PABP, (ii) the AUF1 binding to poly(A) does not change when the polyadenylated probe contains the GM-CSF (granulocyte/macrophage-colony stimulating factor) ARE, suggesting that, in vitro, the AUF1-poly(A) association was independent of the ARE sequence itself. In vitro, the binding of AUF1 isoforms to poly(A) displayed oligomeric and co-operative properties and AUF1 efficiently displaced PABP from the poly(A). Finally, the AUF1 molar concentration in HeLa cytoplasm was only 2-fold lower than that of PABP, whereas in the nucleus, its molar concentration was similar to that of PABP. These in vitro results suggest that, in vivo, AUF1 could compete with PABP for the binding to poly(A). Altogether, our results may suggest a role for AUF1 in controlling PABP-poly(A) tail association.
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Affiliation(s)
- Francis Sagliocco
- *INSERM, E362, Bordeaux, F-33076 France; Université Victor Segalen Bordeaux 2, Bordeaux, F-33076 France
- †IFR66, Bordeaux, F-33076 France
| | - Benoît Laloo
- *INSERM, E362, Bordeaux, F-33076 France; Université Victor Segalen Bordeaux 2, Bordeaux, F-33076 France
- †IFR66, Bordeaux, F-33076 France
| | - Bertrand Cosson
- ‡CNRS, UMR 6061, Rennes F-35043, France; Université Rennes I, Rennes, F-35043 France
| | - Laurence Laborde
- *INSERM, E362, Bordeaux, F-33076 France; Université Victor Segalen Bordeaux 2, Bordeaux, F-33076 France
- †IFR66, Bordeaux, F-33076 France
| | - Michel Castroviejo
- †IFR66, Bordeaux, F-33076 France
- §CNRS, UMR 5097, Bordeaux, F-33076 France; Université Victor Segalen Bordeaux 2, Bordeaux, F-33076 France
| | - Jean Rosenbaum
- *INSERM, E362, Bordeaux, F-33076 France; Université Victor Segalen Bordeaux 2, Bordeaux, F-33076 France
- †IFR66, Bordeaux, F-33076 France
| | - Jean Ripoche
- *INSERM, E362, Bordeaux, F-33076 France; Université Victor Segalen Bordeaux 2, Bordeaux, F-33076 France
- †IFR66, Bordeaux, F-33076 France
| | - Christophe Grosset
- *INSERM, E362, Bordeaux, F-33076 France; Université Victor Segalen Bordeaux 2, Bordeaux, F-33076 France
- †IFR66, Bordeaux, F-33076 France
- To whom correspondence should be addressed (email )
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Abstract
CUG-BP1 [CUG-binding protein 1 also called CELF (CUG-BP1 and ETR3 like factors) 1] is a human RNA-binding protein that has been implicated in the control of splicing and mRNA translation. The Xenopus homologue [EDEN-BP (embryo deadenylation element-binding protein)] is required for rapid deadenylation of certain maternal mRNAs just after fertilization. A variety of sequence elements have been described as target sites for these two proteins but their binding specificity is still controversial. Using a SELEX (systematic evolution of ligand by exponential enrichment) procedure and recombinant CUG-BP1 we selected two families of aptamers. Surface plasmon resonance and electrophoretic mobility-shift assays showed that these two families differed in their ability to bind CUG-BP1. Furthermore, the selected high-affinity aptamers form two complexes with CUG-BP1 in electrophoretic mobility assays whereas those that bind with low affinity only form one complex. The validity of the distinction between the two families of aptamers was confirmed by a functional in vivo deadenylation assay. Only those aptamers that bound CUG-BP1 with high affinity conferred deadenylation on a reporter mRNA. These high-affinity RNAs are characterized by a richness in UGU motifs. Using these binding site characteristics we identified the Xenopus maternal mRNA encoding the MAPK (mitogen-activated protein kinase) phosphatase (XCl100alpha) as a substrate for EDEN-BP. In conclusion, high-affinity CUG-BP1 binding sites are sequence elements at least 30 nucleotides in length that are enriched in combinations of U and G nucleotides and contain at least 4 UGU trinucleotide motifs. Such sequence elements are functionally competent to target an RNA for deadenylation in vivo.
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Affiliation(s)
- Julien Marquis
- *Généthon, CNRS UMR 8115, 1 bis rue de l'Internationale 91002 Evry cedex 2, France
| | - Luc Paillard
- †CNRS UMR 6061, Génétique et Développement, IFR 140 GFAS, Université de Rennes 1, Faculté de Médecine, 2 Avenue Léon Bernard, CS 34317, 35043 Rennes Cedex, France
| | - Yann Audic
- †CNRS UMR 6061, Génétique et Développement, IFR 140 GFAS, Université de Rennes 1, Faculté de Médecine, 2 Avenue Léon Bernard, CS 34317, 35043 Rennes Cedex, France
| | - Bertrand Cosson
- †CNRS UMR 6061, Génétique et Développement, IFR 140 GFAS, Université de Rennes 1, Faculté de Médecine, 2 Avenue Léon Bernard, CS 34317, 35043 Rennes Cedex, France
| | - Olivier Danos
- *Généthon, CNRS UMR 8115, 1 bis rue de l'Internationale 91002 Evry cedex 2, France
| | - Christine Le Bec
- *Généthon, CNRS UMR 8115, 1 bis rue de l'Internationale 91002 Evry cedex 2, France
| | - H. Beverley Osborne
- †CNRS UMR 6061, Génétique et Développement, IFR 140 GFAS, Université de Rennes 1, Faculté de Médecine, 2 Avenue Léon Bernard, CS 34317, 35043 Rennes Cedex, France
- To whom correspondence should be addressed (email )
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Sodergren E, Weinstock GM, Davidson EH, Cameron RA, Gibbs RA, Angerer RC, Angerer LM, Arnone MI, Burgess DR, Burke RD, Coffman JA, Dean M, Elphick MR, Ettensohn CA, Foltz KR, Hamdoun A, Hynes RO, Klein WH, Marzluff W, McClay DR, Morris RL, Mushegian A, Rast JP, Smith LC, Thorndyke MC, Vacquier VD, Wessel GM, Wray G, Zhang L, Elsik CG, Ermolaeva O, Hlavina W, Hofmann G, Kitts P, Landrum MJ, Mackey AJ, Maglott D, Panopoulou G, Poustka AJ, Pruitt K, Sapojnikov V, Song X, Souvorov A, Solovyev V, Wei Z, Whittaker CA, Worley K, Durbin KJ, Shen Y, Fedrigo O, Garfield D, Haygood R, Primus A, Satija R, Severson T, Gonzalez-Garay ML, Jackson AR, Milosavljevic A, Tong M, Killian CE, Livingston BT, Wilt FH, Adams N, Bellé R, Carbonneau S, Cheung R, Cormier P, Cosson B, Croce J, Fernandez-Guerra A, Genevière AM, Goel M, Kelkar H, Morales J, Mulner-Lorillon O, Robertson AJ, Goldstone JV, Cole B, Epel D, Gold B, Hahn ME, Howard-Ashby M, Scally M, Stegeman JJ, Allgood EL, Cool J, Judkins KM, McCafferty SS, Musante AM, Obar RA, Rawson AP, Rossetti BJ, Gibbons IR, Hoffman MP, Leone A, Istrail S, Materna SC, Samanta MP, Stolc V, Tongprasit W, Tu Q, Bergeron KF, Brandhorst BP, Whittle J, Berney K, Bottjer DJ, Calestani C, Peterson K, Chow E, Yuan QA, Elhaik E, Graur D, Reese JT, Bosdet I, Heesun S, Marra MA, Schein J, Anderson MK, Brockton V, Buckley KM, Cohen AH, Fugmann SD, Hibino T, Loza-Coll M, Majeske AJ, Messier C, Nair SV, Pancer Z, Terwilliger DP, Agca C, Arboleda E, Chen N, Churcher AM, Hallböök F, Humphrey GW, Idris MM, Kiyama T, Liang S, Mellott D, Mu X, Murray G, Olinski RP, Raible F, Rowe M, Taylor JS, Tessmar-Raible K, Wang D, Wilson KH, Yaguchi S, Gaasterland T, Galindo BE, Gunaratne HJ, Juliano C, Kinukawa M, Moy GW, Neill AT, Nomura M, Raisch M, Reade A, Roux MM, Song JL, Su YH, Townley IK, Voronina E, Wong JL, Amore G, Branno M, Brown ER, Cavalieri V, Duboc V, Duloquin L, Flytzanis C, Gache C, Lapraz F, Lepage T, Locascio A, Martinez P, Matassi G, Matranga V, Range R, Rizzo F, Röttinger E, Beane W, Bradham C, Byrum C, Glenn T, Hussain S, Manning G, Miranda E, Thomason R, Walton K, Wikramanayke A, Wu SY, Xu R, Brown CT, Chen L, Gray RF, Lee PY, Nam J, Oliveri P, Smith J, Muzny D, Bell S, Chacko J, Cree A, Curry S, Davis C, Dinh H, Dugan-Rocha S, Fowler J, Gill R, Hamilton C, Hernandez J, Hines S, Hume J, Jackson L, Jolivet A, Kovar C, Lee S, Lewis L, Miner G, Morgan M, Nazareth LV, Okwuonu G, Parker D, Pu LL, Thorn R, Wright R. The genome of the sea urchin Strongylocentrotus purpuratus. Science 2006; 314:941-52. [PMID: 17095691 PMCID: PMC3159423 DOI: 10.1126/science.1133609] [Citation(s) in RCA: 795] [Impact Index Per Article: 44.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/19/2023]
Abstract
We report the sequence and analysis of the 814-megabase genome of the sea urchin Strongylocentrotus purpuratus, a model for developmental and systems biology. The sequencing strategy combined whole-genome shotgun and bacterial artificial chromosome (BAC) sequences. This use of BAC clones, aided by a pooling strategy, overcame difficulties associated with high heterozygosity of the genome. The genome encodes about 23,300 genes, including many previously thought to be vertebrate innovations or known only outside the deuterostomes. This echinoderm genome provides an evolutionary outgroup for the chordates and yields insights into the evolution of deuterostomes.
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23
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Fernandez-Guerra A, Aze A, Morales J, Mulner-Lorillon O, Cosson B, Cormier P, Bradham C, Adams N, Robertson AJ, Marzluff WF, Coffman JA, Genevière AM. The genomic repertoire for cell cycle control and DNA metabolism in S. purpuratus. Dev Biol 2006; 300:238-51. [PMID: 17078944 DOI: 10.1016/j.ydbio.2006.09.012] [Citation(s) in RCA: 40] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/30/2006] [Revised: 09/06/2006] [Accepted: 09/07/2006] [Indexed: 02/06/2023]
Abstract
A search of the Strongylocentrotus purpuratus genome for genes associated with cell cycle control and DNA metabolism shows that the known repertoire of these genes is conserved in the sea urchin, although with fewer family members represented than in vertebrates, and with some cases of echinoderm-specific gene diversifications. For example, while homologues of the known cyclins are mostly encoded by single genes in S. purpuratus (unlike vertebrates, which have multiple isoforms), there are additional genes encoding novel cyclins of the B and K/L types. Almost all known cyclin-dependent kinases (CDKs) or CDK-like proteins have an orthologue in S. purpuratus; CDK3 is one exception, whereas CDK4 and 6 are represented by a single homologue, referred to as CDK4. While the complexity of the two families of mitotic kinases, Polo and Aurora, is close to that found in the nematode, the diversity of the NIMA-related kinases (NEK proteins) approaches that of vertebrates. Among the nine NEK proteins found in S. purpuratus, eight could be assigned orthologues in vertebrates, whereas the ninth is unique to sea urchins. Most known DNA replication, DNA repair and mitotic checkpoint genes are also present, as are homologues of the pRB (two) and p53 (one) tumor suppressors. Interestingly, the p21/p27 family of CDK inhibitors is represented by one homologue, whereas the INK4 and ARF families of tumor suppressors appear to be absent, suggesting that these evolved only in vertebrates. Our results suggest that, while the cell cycle control mechanisms known from other animals are generally conserved in sea urchin, parts of the machinery have diversified within the echinoderm lineage. The set of genes uncovered in this analysis of the S. purpuratus genome should enhance future research on cell cycle control and developmental regulation in this model.
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Affiliation(s)
- Antonio Fernandez-Guerra
- Observatoire Océanologique de Banyuls-Laboratoire Arago, CNRS-UMR7628/UPMC, 66650 Banyuls-sur-Mer, France.
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Grosset C, Boniface R, Duchez P, Solanilla A, Cosson B, Ripoche J. In vivo studies of translational repression mediated by the granulocyte-macrophage colony-stimulating factor AU-rich element. J Biol Chem 2004; 279:13354-62. [PMID: 14726527 DOI: 10.1074/jbc.m308003200] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
The AU-rich element (ARE) controls the turnover of many unstable mRNAs and their translation. The granulocyte-macrophage colony-stimulating factor (GM-CSF) ARE is known to be a destabilizing element, but its role in translation remains unclear. Here we studied in vivo the role of the GM-CSF ARE on the mRNA and protein expressions of an enhanced green fluorescent protein reporter gene. The GM-CSF ARE had a repressor effect on translation independently of its effect on mRNA levels. In the context of an internal ribosome entry site, the GM-CSF ARE still repressed translation but was no longer functional as a destabilizing element. Gel retardation assays showed that poly(A)-binding protein is displaced from the poly(A) tail when the ARE is present in the 3'-untranslated region. These data suggest that the GM-CSF ARE controls translation and mRNA decay by interfering with poly(A)-binding protein-mediated mRNA circularization.
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Affiliation(s)
- Christophe Grosset
- FRE 2617 CNRS, Université Victor Ségalen Bordeaux 2, 33076 Bordeaux, France.
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Abstract
In eukaryotes transcription and translation takes place in two different compartments separated by the nuclear envelope. Nuclear translation has been reported in several publications, however, all these published results have been criticized, particularly with respect to cytoplasmic contamination of the nuclei. We have investigated the question of nuclear protein synthesis using a different strategy. We microinjected frog oocytes with different DNA and RNA constructs and searched for translation products in nuclei separated from the cytoplasm by microdissection. We have been unable to detect any translation within the nuclei but rather a saturable translation in the perinuclear cytoplasm associated with the isolated nuclei.
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Affiliation(s)
- Bertrand Cosson
- Université de Rennes 1, CNRS UMR 6061, IFR 97, 2, avenue Pr Léon-Bernard, 35043 Rennes cedex, France
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Cosson B, Couturier A, Le Guellec R, Moreau J, Chabelskaya S, Zhouravleva G, Philippe M. Characterization of the poly(A) binding proteins expressed during oogenesis and early development of Xenopus laevis. Biol Cell 2002; 94:217-31. [PMID: 12489691 DOI: 10.1016/s0248-4900(02)01195-4] [Citation(s) in RCA: 28] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
Abstract
During vertebrate oogenesis and early embryogenesis, gene expression is governed mainly by translational control. The recruitment of Poly(A) Binding Protein (PABP) during poly(A) tail lengthening appears to be the key to translational activation during this period of development in Xenopus laevis. We showed that PABP1 and ePABP proteins are both present during oogenesis and early development. We selected ePABP as an eRF3 binding protein in a two-hybrid screening of a X. laevis cDNA library and demonstrated that this protein is associated with translational complexes. It can complement essential functions of the yeast homologue Pab1p. We discuss specific expression patterns of the finely tuned PABP1 and ePABP proteins.
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Affiliation(s)
- Bertrand Cosson
- Université de Rennes 1, CNRS UMR 6061, IFR 97, 2, avenue Pr Léon Bernard, 35043 Rennes cedex, France
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Cosson B, Berkova N, Couturier A, Chabelskaya S, Philippe M, Zhouravleva G. Poly(A)-binding protein and eRF3 are associated in vivo in human and Xenopus cells. Biol Cell 2002; 94:205-16. [PMID: 12489690 DOI: 10.1016/s0248-4900(02)01194-2] [Citation(s) in RCA: 46] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/27/2022]
Abstract
An interaction between human poly(A)-binding protein (PABP) et human eRF3 has been demonstrated using a double-hybrid approach and in vitro assays. Here, we show that the binding of both proteins is conserved through evolution. We also demonstrate that the last 39 C-terminal amino acids of PABP contain the interface that interacts with eRF3. This region includes helix 5, identified by RMN, which is conserved in all known PABPs. Lastly, we demonstrate that eRF3 et PABP molecules interact in vivo.
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Affiliation(s)
- Bertrand Cosson
- Université de Rennes 1, CNRS UMR 6061, IFR 97, avenue du professeur Leon Bernard, 35043 Rennes cedex, France
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Cosson B, Couturier A, Chabelskaya S, Kiktev D, Inge-Vechtomov S, Philippe M, Zhouravleva G. Poly(A)-binding protein acts in translation termination via eukaryotic release factor 3 interaction and does not influence [PSI(+)] propagation. Mol Cell Biol 2002; 22:3301-15. [PMID: 11971964 PMCID: PMC133780 DOI: 10.1128/mcb.22.10.3301-3315.2002] [Citation(s) in RCA: 123] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022] Open
Abstract
Recent studies of translational control suggest that translation termination may not be simply the end of synthesizing a protein but rather be involved in modulating both the translation efficiency and stability of a given transcript. Using recombinant eukaryotic release factor 3 (eRF3) and cellular extracts, we have shown for Saccharomyces cerevisiae that yeast eRF3 and Pab1p can interact. This interaction, mediated by the N+M domain of eRF3 and amino acids 473 to 577 of Pab1p, was demonstrated to be direct by the two-hybrid approach. We confirmed that a genetic interaction exists between eRF3 and Pab1p and showed that Pab1p overexpression enhances the efficiency of termination in SUP35 (eRF3) mutant and [PSI(+)] cells. This effect requires the interaction of Pab1p with eRF3. These data further strengthen the possibility that Pab1p has a role in coupling translation termination events with initiation of translation. Several lines of evidence indicate that Pab1p does not influence [PSI(+)] propagation. First, "[PSI(+)]-no-more" mutations do not affect eRF3-Pab1p two-hybrid interaction. Second, overexpression of PAB1 does not cure the [PSI(+)] phenotype or solubilize detectable amounts of eRF3. Third, prion-curing properties of overexpressed HSP104p, which is required for formation and maintenance of [PSI(+)], were not modified by excess Pab1p.
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Affiliation(s)
- Bertrand Cosson
- Universite de Rennes 1, CNRS UMR 6061, 35043 Rennes Cedex, France
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Zanninelli G, Choudury R, Loréal O, Guyader D, Lescoat G, Arnaud J, Verna R, Cosson B, Singh S, Hider RC, Brissot P. Novel orally active iron chelators (3-hydroxypyridin-4-ones) enhance the biliary excretion of plasma non-transferrin-bound iron in rats. J Hepatol 1997; 27:176-84. [PMID: 9252093 DOI: 10.1016/s0168-8278(97)80299-1] [Citation(s) in RCA: 17] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 02/05/2023]
Abstract
BACKGROUND/AIMS It is well documented that levels of plasma non-transferrin-bound iron (NTBI), a particularly toxic form of iron, are increased in iron overload disorders. In light of the pathogenetic importance of NTBI in chronic iron overload, we have studied the ability of new orally active iron chelators to promote the biliary excretion of iron originating as plasma 55Fe-NTBI. METHODS Biliary iron kinetics of plasma 55Fe-labeled NTBI and cumulative recoveries of 55Fe in bile were determined in normal and carbonyl iron-loaded rats receiving a single intragastric dose of iron chelator. These chelators were the novel hydroxypyridin-4-one compounds CP102, CP41, and their respective pro-drugs CP117 and CP165. RESULTS The cumulative recovery of 55Fe in bile of normal rats was increased by 5.2-, 7.9-, 11.5-, and 9.2-fold with CP102, CP117, CP41 and CP165, respectively. In iron overloaded rats, these compounds increased the cumulative recovery by 28.6-, 48.6-, 72.6-, and 32-fold, respectively. All the chelators had a choleretic effect, were metabolized by the liver as demonstrated by HPLC study of bile, and were not cytotoxic since normal plasma transaminase levels were maintained at the end of the experiments. CONCLUSIONS These chelators have potential interest for the treatment of iron overload conditions and may offer advantages over simple N-alkyl-hydroxypyridinones such as deferiprone (CP20, L1).
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Affiliation(s)
- G Zanninelli
- Liver Research Unit, Institut National de la Sante et de la Recherche Médicale INSERM U-49, Pontchaillou University Hospital, Rennes, France.
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