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Piet Q, Droc G, Marande W, Sarah G, Bocs S, Klopp C, Bourge M, Siljak-Yakovlev S, Bouchez O, Lopez-Roques C, Lepers-Andrzejewski S, Bourgois L, Zucca J, Dron M, Besse P, Grisoni M, Jourda C, Charron C. A chromosome-level, haplotype-phased Vanilla planifolia genome highlights the challenge of partial endoreplication for accurate whole-genome assembly. Plant Commun 2022; 3:100330. [PMID: 35617961 PMCID: PMC9482989 DOI: 10.1016/j.xplc.2022.100330] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/30/2021] [Revised: 04/10/2022] [Accepted: 04/27/2022] [Indexed: 06/02/2023]
Abstract
Vanilla planifolia, the species cultivated to produce one of the world's most popular flavors, is highly prone to partial genome endoreplication, which leads to highly unbalanced DNA content in cells. We report here the first molecular evidence of partial endoreplication at the chromosome scale by the assembly and annotation of an accurate haplotype-phased genome of V. planifolia. Cytogenetic data demonstrated that the diploid genome size is 4.09 Gb, with 16 chromosome pairs, although aneuploid cells are frequently observed. Using PacBio HiFi and optical mapping, we assembled and phased a diploid genome of 3.4 Gb with a scaffold N50 of 1.2 Mb and 59 128 predicted protein-coding genes. The atypical k-mer frequencies and the uneven sequencing depth observed agreed with our expectation of unbalanced genome representation. Sixty-seven percent of the genes were scattered over only 30% of the genome, putatively linking gene-rich regions and the endoreplication phenomenon. By contrast, low-coverage regions (non-endoreplicated) were rich in repeated elements but also contained 33% of the annotated genes. Furthermore, this assembly showed distinct haplotype-specific sequencing depth variation patterns, suggesting complex molecular regulation of endoreplication along the chromosomes. This high-quality, anchored assembly represents 83% of the estimated V. planifolia genome. It provides a significant step toward the elucidation of this complex genome. To support post-genomics efforts, we developed the Vanilla Genome Hub, a user-friendly integrated web portal that enables centralized access to high-throughput genomic and other omics data and interoperable use of bioinformatics tools.
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Affiliation(s)
- Quentin Piet
- CIRAD, UMR PVBMT, 97410 Saint-Pierre, La Réunion, France
| | - Gaetan Droc
- CIRAD, UMR AGAP Institut, 34398 Montpellier, France; UMR AGAP Institut, Univ Montpellier, CIRAD, INRAE, Institut Agro, 34398 Montpellier, France; French Institute of Bioinformatics (IFB) - South Green Bioinformatics Platform, Bioversity, CIRAD, INRAE, IRD, 34398 Montpellier, France.
| | | | - Gautier Sarah
- French Institute of Bioinformatics (IFB) - South Green Bioinformatics Platform, Bioversity, CIRAD, INRAE, IRD, 34398 Montpellier, France; AGAP, Univ. Montpellier, CIRAD, INRAE, Montpellier SupAgro, Montpellier, France
| | - Stéphanie Bocs
- CIRAD, UMR AGAP Institut, 34398 Montpellier, France; UMR AGAP Institut, Univ Montpellier, CIRAD, INRAE, Institut Agro, 34398 Montpellier, France; French Institute of Bioinformatics (IFB) - South Green Bioinformatics Platform, Bioversity, CIRAD, INRAE, IRD, 34398 Montpellier, France
| | - Christophe Klopp
- Plateforme Bioinformatique, Genotoul, BioinfoMics, UR875 Biométrie et Intelligence Artificielle, INRAE, Castanet-Tolosan, France
| | - Mickael Bourge
- Cytometry Facility, Imagerie-Gif, Université Paris-Saclay, CEA, CNRS, Institute for Integrative Biology of the Cell (I2BC), 91198 Gif-sur-Yvette, France
| | - Sonja Siljak-Yakovlev
- Université Paris-Saclay, CNRS, AgroParisTech, Ecologie Systématique Evolution (ESE), 91190 Gif-sur-Yvette, France
| | | | | | | | | | - Joseph Zucca
- Département Biotechnologie, V. Mane Fils, 06620 Le Bar Sur Loup, France
| | - Michel Dron
- Université Paris-Saclay, CNRS, INRAE, Univ. Evry, Institute of Plant Sciences Paris-Saclay (IPS2), 91405 Orsay, France
| | - Pascale Besse
- Université de la Réunion, UMR PVBMT, Saint-Pierre, La Réunion, France
| | | | - Cyril Jourda
- CIRAD, UMR PVBMT, 97410 Saint-Pierre, La Réunion, France.
| | - Carine Charron
- CIRAD, UMR PVBMT, 97410 Saint-Pierre, La Réunion, France
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2
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Chalvin C, Drevensek S, Gilard F, Mauve C, Chollet C, Morin H, Nicol E, Héripré E, Kriegshauser L, Gakière B, Dron M, Bendahmane A, Boualem A. Sclareol and linalyl acetate are produced by glandular trichomes through the MEP pathway. Hortic Res 2021; 8:206. [PMID: 34593779 PMCID: PMC8484277 DOI: 10.1038/s41438-021-00640-w] [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] [Figures] [Subscribe] [Scholar Register] [Received: 04/10/2021] [Revised: 07/09/2021] [Accepted: 07/22/2021] [Indexed: 06/13/2023]
Abstract
Sclareol, an antifungal specialized metabolite produced by clary sage, Salvia sclarea, is the starting plant natural molecule used for the hemisynthesis of the perfume ingredient ambroxide. Sclareol is mainly produced in clary sage flower calyces; however, the cellular localization of the sclareol biosynthesis remains unknown. To elucidate the site of sclareol biosynthesis, we analyzed its spatial distribution in the clary sage calyx epidermis using laser desorption/ionization mass spectrometry imaging (LDI-FTICR-MSI) and investigated the expression profile of sclareol biosynthesis genes in isolated glandular trichomes (GTs). We showed that sclareol specifically accumulates in GTs' gland cells in which sclareol biosynthesis genes are strongly expressed. We next isolated a glabrous beardless mutant and demonstrate that more than 90% of the sclareol is produced by the large capitate GTs. Feeding experiments, using 1-13C-glucose, and specific enzyme inhibitors further revealed that the methylerythritol-phosphate (MEP) biosynthetic pathway is the main source of isopentenyl diphosphate (IPP) precursor used for the biosynthesis of sclareol. Our findings demonstrate that sclareol is an MEP-derived diterpene produced by large capitate GTs in clary sage emphasing the role of GTs as biofactories dedicated to the production of specialized metabolites.
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Affiliation(s)
- Camille Chalvin
- Université Paris-Saclay, CNRS, INRAE, Univ Evry, Institute of Plant Sciences Paris-Saclay (IPS2), 91405, Orsay, France
| | - Stéphanie Drevensek
- Université Paris-Saclay, CNRS, INRAE, Univ Evry, Institute of Plant Sciences Paris-Saclay (IPS2), 91405, Orsay, France
| | - Françoise Gilard
- Université Paris-Saclay, CNRS, INRAE, Univ Evry, Institute of Plant Sciences Paris-Saclay (IPS2), 91405, Orsay, France
| | - Caroline Mauve
- Université Paris-Saclay, CNRS, INRAE, Univ Evry, Institute of Plant Sciences Paris-Saclay (IPS2), 91405, Orsay, France
| | - Christel Chollet
- Université Paris-Saclay, CNRS, INRAE, Univ Evry, Institute of Plant Sciences Paris-Saclay (IPS2), 91405, Orsay, France
| | - Halima Morin
- Université Paris-Saclay, CNRS, INRAE, Univ Evry, Institute of Plant Sciences Paris-Saclay (IPS2), 91405, Orsay, France
| | - Edith Nicol
- Molecular Chemistry Laboratory (LCM), UMR 9168, CNRS, Ecole Polytechnique, Institut Polytechnique de Paris, Route de Saclay, 91128, Palaiseau Cedex, France
| | - Eva Héripré
- Laboratory of Mechanics of Soils, Structures and Materials (MSSMAT), UMR 8579, CNRS, Ecole CentraleSupélec, Université Paris-Saclay, Bâtiment Eiffel, 8-10 rue Joliot-Curie, 91190, Gif-Sur-Yvette, France
| | - Lucie Kriegshauser
- Université Paris-Saclay, CNRS, INRAE, Univ Evry, Institute of Plant Sciences Paris-Saclay (IPS2), 91405, Orsay, France
| | - Bertrand Gakière
- Université Paris-Saclay, CNRS, INRAE, Univ Evry, Institute of Plant Sciences Paris-Saclay (IPS2), 91405, Orsay, France
| | - Michel Dron
- Université Paris-Saclay, CNRS, INRAE, Univ Evry, Institute of Plant Sciences Paris-Saclay (IPS2), 91405, Orsay, France
| | - Abdelhafid Bendahmane
- Université Paris-Saclay, CNRS, INRAE, Univ Evry, Institute of Plant Sciences Paris-Saclay (IPS2), 91405, Orsay, France
| | - Adnane Boualem
- Université Paris-Saclay, CNRS, INRAE, Univ Evry, Institute of Plant Sciences Paris-Saclay (IPS2), 91405, Orsay, France.
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3
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Chalvin C, Drevensek S, Chollet C, Gilard F, Šolić EM, Dron M, Bendahmane A, Boualem A, Cornille A. Study of the genetic and phenotypic variation among wild and cultivated clary sages provides interesting avenues for breeding programs of a perfume, medicinal and aromatic plant. PLoS One 2021; 16:e0248954. [PMID: 34288908 PMCID: PMC8294528 DOI: 10.1371/journal.pone.0248954] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/22/2020] [Accepted: 03/09/2021] [Indexed: 11/18/2022] Open
Abstract
A road-map of the genetic and phenotypic diversities in both crops and their wild related species can help identifying valuable genetic resources for further crop breeding. The clary sage (Salvia sclarea L.), a perfume, medicinal and aromatic plant, is used for sclareol production and ornamental purposes. Despite its wide use in the field of cosmetics, the phenotypic and genetic diversity of wild and cultivated clary sages remains to be explored. We characterized the genetic and phenotypic variation of a collection of six wild S. sclarea populations from Croatia, sampled along an altitudinal gradient, and, of populations of three S. sclarea cultivars. We showed low level of genetic diversity for the two S. sclarea traditional cultivars used for essential oil production and for ornamental purposes, respectively. In contrast, a recent cultivar resulting from new breeding methods, which involve hybridizations among several genotypes rather than traditional recurrent selection and self-crosses over time, showed high genetic diversity. We also observed a marked phenotypic differentiation for the ornamental clary sage compared with other cultivated and wild clary sages. Instead, the two cultivars used for essential oil production, a traditional and a recent one, respectively, were not phenotypically differentiated from the wild Croatian populations. Our results also featured some wild populations with high sclareol content and early-flowering phenotypes as good candidates for future breeding programs. This study opens up perspectives for basic research aiming at understanding the impact of breeding methods on clary sage evolution, and highlights interesting avenues for clary breeding programs.
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Affiliation(s)
- Camille Chalvin
- Institute of Plant Sciences Paris‐Saclay (IPS2), UMR 9213/UMR 1403, Université Paris‐Saclay, Orsay, France
| | - Stéphanie Drevensek
- Institute of Plant Sciences Paris‐Saclay (IPS2), UMR 9213/UMR 1403, Université Paris‐Saclay, Orsay, France
| | - Christel Chollet
- Institute of Plant Sciences Paris‐Saclay (IPS2), UMR 9213/UMR 1403, Université Paris‐Saclay, Orsay, France
| | - Françoise Gilard
- Institute of Plant Sciences Paris‐Saclay (IPS2), UMR 9213/UMR 1403, Université Paris‐Saclay, Orsay, France
| | | | - Michel Dron
- Institute of Plant Sciences Paris‐Saclay (IPS2), UMR 9213/UMR 1403, Université Paris‐Saclay, Orsay, France
| | - Abdelhafid Bendahmane
- Institute of Plant Sciences Paris‐Saclay (IPS2), UMR 9213/UMR 1403, Université Paris‐Saclay, Orsay, France
| | - Adnane Boualem
- Institute of Plant Sciences Paris‐Saclay (IPS2), UMR 9213/UMR 1403, Université Paris‐Saclay, Orsay, France
- * E-mail:
| | - Amandine Cornille
- Université Paris-Saclay, INRAE, CNRS, AgroParisTech, GQE - Le Moulon, Gif-sur-Yvette, France
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4
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Munoz-Montesino C, Larkem D, Barbereau C, Igel-Egalon A, Truchet S, Jacquet E, Nhiri N, Moudjou M, Sizun C, Rezaei H, Béringue V, Dron M. A seven-residue deletion in PrP leads to generation of a spontaneous prion formed from C-terminal C1 fragment of PrP. J Biol Chem 2020; 295:14025-14039. [PMID: 32788216 DOI: 10.1074/jbc.ra120.014738] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [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: 06/08/2020] [Revised: 07/27/2020] [Indexed: 12/17/2022] Open
Abstract
Prions result from a drastic conformational change of the host-encoded cellular prion protein (PrP), leading to the formation of β-sheet-rich, insoluble, and protease-resistant self-replicating assemblies (PrPSc). The cellular and molecular mechanisms involved in spontaneous prion formation in sporadic and inherited human prion diseases or equivalent animal diseases are poorly understood, in part because cell models of spontaneously forming prions are currently lacking. Here, extending studies on the role of the H2 α-helix C terminus of PrP, we found that deletion of the highly conserved 190HTVTTTT196 segment of ovine PrP led to spontaneous prion formation in the RK13 rabbit kidney cell model. On long-term passage, the mutant cells stably produced proteinase K (PK)-resistant, insoluble, and aggregated assemblies that were infectious for naïve cells expressing either the mutant protein or other PrPs with slightly different deletions in the same area. The electrophoretic pattern of the PK-resistant core of the spontaneous prion (ΔSpont) contained mainly C-terminal polypeptides akin to C1, the cell-surface anchored C-terminal moiety of PrP generated by natural cellular processing. RK13 cells expressing solely the Δ190-196 C1 PrP construct, in the absence of the full-length protein, were susceptible to ΔSpont prions. ΔSpont infection induced the conversion of the mutated C1 into a PK-resistant and infectious form perpetuating the biochemical characteristics of ΔSpont prion. In conclusion, this work provides a unique cell-derived system generating spontaneous prions and provides evidence that the 113 C-terminal residues of PrP are sufficient for a self-propagating prion entity.
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Affiliation(s)
- Carola Munoz-Montesino
- Université Paris-Saclay, Institut National de Recherche pour l'Agriculture, l'Alimentation et l'Environnement, Université de Versailles Saint-Quentin-en-Yvelines, Virologie et Immunologie Moléculaires, Jouy-en-Josas, France
| | - Djabir Larkem
- Université Paris-Saclay, Institut National de Recherche pour l'Agriculture, l'Alimentation et l'Environnement, Université de Versailles Saint-Quentin-en-Yvelines, Virologie et Immunologie Moléculaires, Jouy-en-Josas, France
| | - Clément Barbereau
- Université Paris-Saclay, Institut National de Recherche pour l'Agriculture, l'Alimentation et l'Environnement, Université de Versailles Saint-Quentin-en-Yvelines, Virologie et Immunologie Moléculaires, Jouy-en-Josas, France
| | - Angélique Igel-Egalon
- Université Paris-Saclay, Institut National de Recherche pour l'Agriculture, l'Alimentation et l'Environnement, Université de Versailles Saint-Quentin-en-Yvelines, Virologie et Immunologie Moléculaires, Jouy-en-Josas, France
| | - Sandrine Truchet
- Université Paris-Saclay, Institut National de Recherche pour l'Agriculture, l'Alimentation et l'Environnement, Université de Versailles Saint-Quentin-en-Yvelines, Virologie et Immunologie Moléculaires, Jouy-en-Josas, France
| | - Eric Jacquet
- Institut de Chimie des Substances Naturelles, CNRS, Université Paris-Saclay, Gif-sur-Yvette, France
| | - Naïma Nhiri
- Institut de Chimie des Substances Naturelles, CNRS, Université Paris-Saclay, Gif-sur-Yvette, France
| | - Mohammed Moudjou
- Université Paris-Saclay, Institut National de Recherche pour l'Agriculture, l'Alimentation et l'Environnement, Université de Versailles Saint-Quentin-en-Yvelines, Virologie et Immunologie Moléculaires, Jouy-en-Josas, France
| | - Christina Sizun
- Institut de Chimie des Substances Naturelles, CNRS, Université Paris-Saclay, Gif-sur-Yvette, France
| | - Human Rezaei
- Université Paris-Saclay, Institut National de Recherche pour l'Agriculture, l'Alimentation et l'Environnement, Université de Versailles Saint-Quentin-en-Yvelines, Virologie et Immunologie Moléculaires, Jouy-en-Josas, France
| | - Vincent Béringue
- Université Paris-Saclay, Institut National de Recherche pour l'Agriculture, l'Alimentation et l'Environnement, Université de Versailles Saint-Quentin-en-Yvelines, Virologie et Immunologie Moléculaires, Jouy-en-Josas, France
| | - Michel Dron
- Université Paris-Saclay, Institut National de Recherche pour l'Agriculture, l'Alimentation et l'Environnement, Université de Versailles Saint-Quentin-en-Yvelines, Virologie et Immunologie Moléculaires, Jouy-en-Josas, France
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5
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Chalvin C, Drevensek S, Dron M, Bendahmane A, Boualem A. Genetic Control of Glandular Trichome Development. Trends Plant Sci 2020; 25:477-487. [PMID: 31983619 DOI: 10.1016/j.tplants.2019.12.025] [Citation(s) in RCA: 62] [Impact Index Per Article: 15.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/02/2019] [Revised: 12/06/2019] [Accepted: 12/20/2019] [Indexed: 05/28/2023]
Abstract
Plant glandular trichomes are epidermal secretory structures producing various specialized metabolites. These metabolites are involved in plant adaptation to its environment and many of them have remarkable properties exploited by fragrance, flavor, and pharmaceutical industries. The identification of genes controlling glandular trichome development is of high interest to understand how plants produce specialized metabolites. Our knowledge about this developmental process is still limited, but genes controlling glandular trichome initiation and morphogenesis have recently been identified. In particular, R2R3-MYB and HD-ZIP IV transcription factors appear to play essential roles in glandular trichome initiation in Artemisia annua and tomato. In this review, we focus on the results obtained in these two species and we propose genetic regulation models integrating these data.
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Affiliation(s)
- Camille Chalvin
- Université Paris-Saclay, INRAE, CNRS, Univ Evry, Institute of Plant Sciences Paris-Saclay (IPS2), 91405, Orsay, France
| | - Stéphanie Drevensek
- Université Paris-Saclay, INRAE, CNRS, Univ Evry, Institute of Plant Sciences Paris-Saclay (IPS2), 91405, Orsay, France
| | - Michel Dron
- Université Paris-Saclay, INRAE, CNRS, Univ Evry, Institute of Plant Sciences Paris-Saclay (IPS2), 91405, Orsay, France
| | - Abdelhafid Bendahmane
- Université Paris-Saclay, INRAE, CNRS, Univ Evry, Institute of Plant Sciences Paris-Saclay (IPS2), 91405, Orsay, France
| | - Adnane Boualem
- Université Paris-Saclay, INRAE, CNRS, Univ Evry, Institute of Plant Sciences Paris-Saclay (IPS2), 91405, Orsay, France.
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6
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Hirsch TZ, Martin-Lannerée S, Reine F, Hernandez-Rapp J, Herzog L, Dron M, Privat N, Passet B, Halliez S, Villa-Diaz A, Lacroux C, Klein V, Haïk S, Andréoletti O, Torres JM, Vilotte JL, Béringue V, Mouillet-Richard S. Epigenetic Control of the Notch and Eph Signaling Pathways by the Prion Protein: Implications for Prion Diseases. Mol Neurobiol 2018; 56:2159-2173. [PMID: 29998397 DOI: 10.1007/s12035-018-1193-7] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2017] [Accepted: 06/26/2018] [Indexed: 12/12/2022]
Abstract
Among the ever-growing number of self-replicating proteins involved in neurodegenerative diseases, the prion protein PrP remains the most infamous for its central role in transmissible spongiform encephalopathies (TSEs). In these diseases, pathogenic prions propagate through a seeding mechanism, where normal PrPC molecules are converted into abnormally folded scrapie isoforms termed PrPSc. Since its discovery over 30 years ago, much advance has contributed to define the host-encoded cellular prion protein PrPC as a critical relay of prion-induced neuronal cell demise. A current consensual view is that the conversion of PrPC into PrPSc in neuronal cells diverts the former from its normal function with subsequent molecular alterations affecting synaptic plasticity. Here, we report that prion infection is associated with reduced expression of key effectors of the Notch pathway in vitro and in vivo, recapitulating changes fostered by the absence of PrPC. We further show that both prion infection and PrPC depletion promote drastic alterations in the expression of a defined set of Eph receptors and their ephrin ligands, which represent important players in synaptic function. Our data indicate that defects in the Notch and Eph axes can be mitigated in response to histone deacetylase inhibition in PrPC-depleted as well as prion-infected cells. We thus conclude that infectious prions cause a loss-of-function phenotype with respect to Notch and Eph signaling and that these alterations are sustained by epigenetic mechanisms.
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Affiliation(s)
- Théo Z Hirsch
- INSERM UMR 1124, 75006, Paris, France
- Université Paris Descartes, Sorbonne Paris Cité, UMR 1124, 75006, Paris, France
- INSERM U1162, 75010, Paris, France
| | - Séverine Martin-Lannerée
- INSERM UMR 1124, 75006, Paris, France
- Université Paris Descartes, Sorbonne Paris Cité, UMR 1124, 75006, Paris, France
| | - Fabienne Reine
- INRA, Université Paris-Saclay, UR 892 Virologie Immunologie Moléculaires, 78350, Jouy-en-Josas, France
| | - Julia Hernandez-Rapp
- INSERM UMR 1124, 75006, Paris, France
- Université Paris Descartes, Sorbonne Paris Cité, UMR 1124, 75006, Paris, France
- Centre de Recherche du CHU de Québec, Université Laval, Québec, G1V4G2, Québec, Canada
| | - Laetitia Herzog
- INRA, Université Paris-Saclay, UR 892 Virologie Immunologie Moléculaires, 78350, Jouy-en-Josas, France
| | - Michel Dron
- INRA, Université Paris-Saclay, UR 892 Virologie Immunologie Moléculaires, 78350, Jouy-en-Josas, France
| | - Nicolas Privat
- INSERM UMR 1127, CNRS UMR 7225, 75013, Paris, France
- Institut du Cerveau et de la Moelle épinière, ICM, Inserm U 1127, CNRS UMR 7225, Sorbonne Université, F-75013, Paris, France
| | - Bruno Passet
- INRA UMR1313, Génétique Animale et Biologie Intégrative, 78350, Jouy-en-Josas, France
| | - Sophie Halliez
- INRA, Université Paris-Saclay, UR 892 Virologie Immunologie Moléculaires, 78350, Jouy-en-Josas, France
- INSERM, UMR-S1172, Lille University, 59045, Lille, France
| | - Ana Villa-Diaz
- Centro de Investigación en Sanidad Animal-INIA, 28130, Madrid, Spain
| | | | - Victor Klein
- INSERM UMR 1124, 75006, Paris, France
- Université Paris Descartes, Sorbonne Paris Cité, UMR 1124, 75006, Paris, France
| | - Stéphane Haïk
- INSERM UMR 1127, CNRS UMR 7225, 75013, Paris, France
- Institut du Cerveau et de la Moelle épinière, ICM, Inserm U 1127, CNRS UMR 7225, Sorbonne Université, F-75013, Paris, France
| | | | - Juan-Maria Torres
- Centro de Investigación en Sanidad Animal-INIA, 28130, Madrid, Spain
| | - Jean-Luc Vilotte
- INRA UMR1313, Génétique Animale et Biologie Intégrative, 78350, Jouy-en-Josas, France
| | | | - Sophie Mouillet-Richard
- INSERM UMR 1124, 75006, Paris, France.
- Université Paris Descartes, Sorbonne Paris Cité, UMR 1124, 75006, Paris, France.
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7
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Brown SC, Bourge M, Maunoury N, Wong M, Wolfe Bianchi M, Lepers-Andrzejewski S, Besse P, Siljak-Yakovlev S, Dron M, Satiat-Jeunemaître B. DNA Remodeling by Strict Partial Endoreplication in Orchids, an Original Process in the Plant Kingdom. Genome Biol Evol 2017; 9:1051-1071. [PMID: 28419219 PMCID: PMC5546068 DOI: 10.1093/gbe/evx063] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.6] [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] [Accepted: 04/11/2017] [Indexed: 12/12/2022] Open
Abstract
DNA remodeling during endoreplication appears to be a strong developmental characteristic
in orchids. In this study, we analyzed DNA content and nuclei in 41 species of orchids to
further map the genome evolution in this plant family. We demonstrate that the DNA
remodeling observed in 36 out of 41 orchids studied corresponds to strict partial
endoreplication. Such process is developmentally regulated in each wild
species studied. Cytometry data analyses allowed us to propose a model where nuclear
states 2C, 4E, 8E, etc. form a series comprising a fixed proportion, the euploid genome
2C, plus 2–32 additional copies of a complementary part of the genome. The fixed
proportion ranged from 89% of the genome in Vanilla mexicana down to 19%
in V. pompona, the lowest value for all 148 orchids reported.
Insterspecific hybridization did not suppress this phenomenon. Interestingly, this process
was not observed in mass-produced epiphytes. Nucleolar volumes grow with the number of
endocopies present, coherent with high transcription activity in endoreplicated nuclei.
Our analyses suggest species-specific chromatin rearrangement. Towards understanding
endoreplication, V. planifolia constitutes a tractable system for
isolating the genomic sequences that confer an advantage via endoreplication from those
that apparently suffice at diploid level.
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Affiliation(s)
- Spencer C Brown
- Institute for Integrative Biology of the Cell (I2BC), CEA, CNRS, Université Paris-Sud, Université Paris-Saclay, Gif-sur-Yvette Cedex, France
| | - Mickaël Bourge
- Institute for Integrative Biology of the Cell (I2BC), CEA, CNRS, Université Paris-Sud, Université Paris-Saclay, Gif-sur-Yvette Cedex, France
| | - Nicolas Maunoury
- Institute for Integrative Biology of the Cell (I2BC), CEA, CNRS, Université Paris-Sud, Université Paris-Saclay, Gif-sur-Yvette Cedex, France
| | - Maurice Wong
- Service du Développement Rural, Papeete Tahiti, French Polynesia, France
| | - Michele Wolfe Bianchi
- Institute for Integrative Biology of the Cell (I2BC), CEA, CNRS, Université Paris-Sud, Université Paris-Saclay, Gif-sur-Yvette Cedex, France
| | | | - Pascale Besse
- UMR 53, PVBMT Université de la Réunion - Cirad, Pôle de Protection des Plantes, St Pierre, France
| | - Sonja Siljak-Yakovlev
- Ecologie Systématique Evolution, Université Paris-Sud, CNRS, AgroParisTech, Université Paris-Saclay, Orsay Cedex, France
| | - Michel Dron
- Institute of Plant Sciences Paris Saclay IPS2, Université Paris-Sud, CNRS, INRA, Université Evry, Université Paris Diderot, Sorbonne Paris-Cité, Université Paris-Saclay, Orsay, France
| | - Béatrice Satiat-Jeunemaître
- Institute for Integrative Biology of the Cell (I2BC), CEA, CNRS, Université Paris-Sud, Université Paris-Saclay, Gif-sur-Yvette Cedex, France
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Munoz-Montesino C, Sizun C, Moudjou M, Herzog L, Reine F, Igel-Egalon A, Barbereau C, Chapuis J, Ciric D, Laude H, Béringue V, Rezaei H, Dron M. A stretch of residues within the protease-resistant core is not necessary for prion structure and infectivity. Prion 2017; 11:25-30. [PMID: 28281924 DOI: 10.1080/19336896.2016.1274851] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022] Open
Abstract
Mapping out regions of PrP influencing prion conversion remains a challenging issue complicated by the lack of prion structure. The portion of PrP associated with infectivity contains the α-helical domain of the correctly folded protein and turns into a β-sheet-rich insoluble core in prions. Deletions performed so far inside this segment essentially prevented the conversion. Recently we found that deletion of the last C-terminal residues of the helix H2 was fully compatible with prion conversion in the RK13-ovPrP cell culture model, using 3 different infecting strains. This was in agreement with preservation of the overall PrPC structure even after removal of up to one-third of this helix. Prions with internal deletion were infectious for cells and mice expressing the wild-type PrP and they retained prion strain-specific characteristics. We thus identified a piece of the prion domain that is neither necessary for the conformational transition of PrPC nor for the formation of a stable prion structure.
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Affiliation(s)
| | - Christina Sizun
- b Institut de Chimie des Substances Naturelles, CNRS, Université Paris Saclay , Gif-sur-Yvette , France
| | | | - Laetitia Herzog
- a VIM, INRA, Université Paris-Saclay , Jouy-en-Josas , France
| | - Fabienne Reine
- a VIM, INRA, Université Paris-Saclay , Jouy-en-Josas , France
| | | | | | - Jérôme Chapuis
- a VIM, INRA, Université Paris-Saclay , Jouy-en-Josas , France
| | - Danica Ciric
- a VIM, INRA, Université Paris-Saclay , Jouy-en-Josas , France
| | - Hubert Laude
- a VIM, INRA, Université Paris-Saclay , Jouy-en-Josas , France
| | | | - Human Rezaei
- a VIM, INRA, Université Paris-Saclay , Jouy-en-Josas , France
| | - Michel Dron
- a VIM, INRA, Université Paris-Saclay , Jouy-en-Josas , France
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9
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Moudjou M, Chapuis J, Mekrouti M, Reine F, Herzog L, Sibille P, Laude H, Vilette D, Andréoletti O, Rezaei H, Dron M, Béringue V. Glycoform-independent prion conversion by highly efficient, cell-based, protein misfolding cyclic amplification. Sci Rep 2016; 6:29116. [PMID: 27384922 PMCID: PMC4935985 DOI: 10.1038/srep29116] [Citation(s) in RCA: 18] [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: 03/09/2016] [Accepted: 06/15/2016] [Indexed: 11/15/2022] Open
Abstract
Prions are formed of misfolded assemblies (PrPSc) of the variably N-glycosylated cellular prion protein (PrPC). In infected species, prions replicate by seeding the conversion and polymerization of host PrPC. Distinct prion strains can be recognized, exhibiting defined PrPSc biochemical properties such as the glycotype and specific biological traits. While strain information is encoded within the conformation of PrPSc assemblies, the storage of the structural information and the molecular requirements for self-perpetuation remain uncertain. Here, we investigated the specific role of PrPC glycosylation status. First, we developed an efficient protein misfolding cyclic amplification method using cells expressing the PrPC species of interest as substrate. Applying the technique to PrPC glycosylation mutants expressing cells revealed that neither PrPC nor PrPSc glycoform stoichiometry was instrumental to PrPSc formation and strainness perpetuation. Our study supports the view that strain properties, including PrPSc glycotype are enciphered within PrPSc structural backbone, not in the attached glycans.
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Affiliation(s)
- Mohammed Moudjou
- VIM, INRA, Université Paris-Saclay, 78350, Jouy-en-Josas, France
| | - Jérôme Chapuis
- VIM, INRA, Université Paris-Saclay, 78350, Jouy-en-Josas, France
| | - Mériem Mekrouti
- VIM, INRA, Université Paris-Saclay, 78350, Jouy-en-Josas, France
| | - Fabienne Reine
- VIM, INRA, Université Paris-Saclay, 78350, Jouy-en-Josas, France
| | - Laetitia Herzog
- VIM, INRA, Université Paris-Saclay, 78350, Jouy-en-Josas, France
| | - Pierre Sibille
- VIM, INRA, Université Paris-Saclay, 78350, Jouy-en-Josas, France
| | - Hubert Laude
- VIM, INRA, Université Paris-Saclay, 78350, Jouy-en-Josas, France
| | - Didier Vilette
- VIM, INRA, Université Paris-Saclay, 78350, Jouy-en-Josas, France.,IHAP, INRA, Ecole Nationale Vétérinaire de Toulouse, 31000, Toulouse, France
| | - Olivier Andréoletti
- IHAP, INRA, Ecole Nationale Vétérinaire de Toulouse, 31000, Toulouse, France
| | - Human Rezaei
- VIM, INRA, Université Paris-Saclay, 78350, Jouy-en-Josas, France
| | - Michel Dron
- VIM, INRA, Université Paris-Saclay, 78350, Jouy-en-Josas, France
| | - Vincent Béringue
- VIM, INRA, Université Paris-Saclay, 78350, Jouy-en-Josas, France
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10
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Chapuis J, Moudjou M, Reine F, Herzog L, Jaumain E, Chapuis C, Quadrio I, Boulliat J, Perret-Liaudet A, Dron M, Laude H, Rezaei H, Béringue V. Emergence of two prion subtypes in ovine PrP transgenic mice infected with human MM2-cortical Creutzfeldt-Jakob disease prions. Acta Neuropathol Commun 2016; 4:10. [PMID: 26847207 PMCID: PMC4743415 DOI: 10.1186/s40478-016-0284-9] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/07/2016] [Accepted: 01/26/2016] [Indexed: 11/23/2022] Open
Abstract
Introduction Mammalian prions are proteinaceous pathogens responsible for a broad range of fatal neurodegenerative diseases in humans and animals. These diseases can occur spontaneously, such as Creutzfeldt-Jakob disease (CJD) in humans, or be acquired or inherited. Prions are primarily formed of macromolecular assemblies of the disease-associated prion protein PrPSc, a misfolded isoform of the host-encoded prion protein PrPC. Within defined host-species, prions can exist as conformational variants or strains. Based on both the M/V polymorphism at codon 129 of PrP and the electrophoretic signature of PrPSc in the brain, sporadic CJD is classified in different subtypes, which may encode different strains. A transmission barrier, the mechanism of which remains unknown, limits prion cross-species propagation. To adapt to the new host, prions have the capacity to ‘mutate’ conformationally, leading to the emergence of a variant with new biological properties. Here, we transmitted experimentally one rare subtype of human CJD, designated cortical MM2 (129 MM with type 2 PrPSc), to transgenic mice overexpressing either human or the VRQ allele of ovine PrPC. Results In marked contrast with the reported absence of transmission to knock-in mice expressing physiological levels of human PrP, this subtype transmitted faithfully to mice overexpressing human PrP, and exhibited unique strain features. Onto the ovine PrP sequence, the cortical MM2 subtype abruptly evolved on second passage, thereby allowing emergence of a pair of strain variants with distinct PrPSc biochemical characteristics and differing tropism for the central and lymphoid tissues. These two strain components exhibited remarkably distinct replicative properties in cell-free amplification assay, allowing the ‘physical’ cloning of the minor, lymphotropic component, and subsequent isolation in ovine PrP mice and RK13 cells. Conclusions Here, we provide in-depth assessment of the transmissibility and evolution of one rare subtype of sporadic CJD upon homologous and heterologous transmission. The notion that the environment or matrix where replication is occurring is key to the selection and preferential amplification of prion substrain components raises new questions on the determinants of prion replication within and between species. These data also further interrogate on the interplay between animal and human prions. Electronic supplementary material The online version of this article (doi:10.1186/s40478-016-0284-9) contains supplementary material, which is available to authorized users.
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11
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Dron M, Bailly Y, Beringue V, Haeberlé AM, Griffond B, Risold PY, Tovey MG, Laude H, Dandoy-Dron F. SCRG1, a Potential Marker of Autophagy in TSE. Autophagy 2014; 2:58-60. [PMID: 16874033 DOI: 10.4161/auto.2228] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.9] [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: 11/19/2022] Open
Abstract
The Scrg1 gene was initially discovered as one of the genes upregulated in transmissible spongiform encephalopathies (TSE). Scrg1 encodes a highly conserved, cysteine-rich protein expressed principally in the central nervous system. The protein is targeted to the Golgi apparatus and large dense-core vesicles/secretory granules in neurons. We have recently shown that the Scrg1 protein is widely induced in neurons of scrapie-infected mice, suggesting that Scrg1 is involved in the host response to stress and/or the death of neurons. At the ultrastructural level, Scrg1 is associated with dictyosomes of the Golgi apparatus and autophagic vacuoles of degenerative neurons. It is well known that apoptosis plays a major role in the events leading to neuronal cell death in TSE. However, autophagy was identified in experimentally induced scrapie a long time ago and was recently reevaluated as a possible cell death program in prion diseases. The consistent association of Scrg1 with autophagic structures typical of scrapie is in agreement with the recruitment of Golgi-specific proteins in this degradation process and we suggest that Scrg1 might be used as a specific probe to identify neuronal autophagy in TSE.
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Affiliation(s)
- Michel Dron
- CNRS UPR-9045, Laboratoire d'Oncologie Virale, Villejuif, France
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12
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Abstract
Upon prion infection, abnormal prion protein (PrP (Sc) ) self-perpetuate by conformational conversion of α-helix-rich PrP (C) into β sheet enriched form, leading to formation and deposition of PrP (Sc) aggregates in affected brains. However the process remains poorly understood at the molecular level and the regions of PrP critical for conversion are still debated. Minimal amino acid substitutions can impair prion replication at many places in PrP. Conversely, we recently showed that bona fide prions could be generated after introduction of eight and up to 16 additional amino acids in the H2-H3 inter-helix loop of PrP. Prion replication also accommodated the insertions of an octapeptide at different places in the last turns of H2. This reverse genetic approach reveals an unexpected tolerance of prions to substantial sequence changes in the protease-resistant part which is associated with infectivity. It also demonstrates that conversion does not require the presence of a specific sequence in the middle of the H2-H3 area. We discuss the implications of our findings according to different structural models proposed for PrP (Sc) and questioned the postulated existence of an N- or C-terminal prion domain in the protease-resistant region.
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13
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Salamat K, Moudjou M, Chapuis J, Herzog L, Jaumain E, Béringue V, Rezaei H, Pastore A, Laude H, Dron M. Integrity of helix 2-helix 3 domain of the PrP protein is not mandatory for prion replication. J Biol Chem 2012; 287:18953-64. [PMID: 22511770 DOI: 10.1074/jbc.m112.341677] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
The process of prion conversion is not yet well understood at the molecular level. The regions critical for the conformational change of PrP remain mostly debated and the extent of sequence change acceptable for prion conversion is poorly documented. To achieve progress on these issues, we applied a reverse genetic approach using the Rov cell system. This allowed us to test the susceptibility of a number of insertion mutants to conversion into prion in the absence of wild-type PrP molecules. We were able to propagate several prions with 8 to 16 extra amino acids, including a polyglycine stretch and His or FLAG tags, inserted in the middle of the protease-resistant fragment. These results demonstrate the possibility to increase the length of the loop between helices H2 and H3 up to 4-fold, without preventing prion replication. They also indicate that this loop probably remains unstructured in PrP(Sc). We also showed that bona fide prions can be produced following insertion of octapeptides in the two C-terminal turns of H2. These insertions do not interfere with the overall fold of the H2-H3 domain indicating that the highly conserved sequence of the terminal part of H2 is not critical for the conversion. Altogether these data showed that the amplitude of modifications acceptable for prion conversion in the core of the globular domain of PrP is much greater than one might have assumed. These observations should help to refine structural models of PrP(Sc) and elucidate the conformational changes underlying prions generation.
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Affiliation(s)
- Khalid Salamat
- INRA, UR892 Virologie Immunologie Moléculaires, F-78350 Jouy-en-Josas, France
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14
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Vivancos J, Spinner L, Mazubert C, Charlot F, Paquet N, Thareau V, Dron M, Nogué F, Charon C. The function of the RNA-binding protein TEL1 in moss reveals ancient regulatory mechanisms of shoot development. Plant Mol Biol 2012; 78:323-336. [PMID: 22170036 DOI: 10.1007/s11103-011-9867-9] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/14/2011] [Accepted: 11/28/2011] [Indexed: 05/31/2023]
Abstract
The shoot represents the basic body plan in land plants. It consists of a repeated structure composed of stems and leaves. Whereas vascular plants generate a shoot in their diploid phase, non-vascular plants such as mosses form a shoot (called the gametophore) in their haploid generation. The evolution of regulatory mechanisms or genetic networks used in the development of these two kinds of shoots is unclear. TERMINAL EAR1-like genes have been involved in diploid shoot development in vascular plants. Here, we show that disruption of PpTEL1 from the moss Physcomitrella patens, causes reduced protonema growth and gametophore initiation, as well as defects in gametophore development. Leafy shoots formed on ΔTEL1 mutants exhibit shorter stems with more leaves per shoot, suggesting an accelerated leaf initiation (shortened plastochron), a phenotype shared with the Poaceae vascular plants TE1 and PLA2/LHD2 mutants. Moreover, the positive correlation between plastochron length and leaf size observed in ΔTEL1 mutants suggests a conserved compensatory mechanism correlating leaf growth and leaf initiation rate that would minimize overall changes in plant biomass. The RNA-binding protein encoded by PpTEL1 contains two N-terminus RNA-recognition motifs, and a third C-terminus non-canonical RRM, specific to TEL proteins. Removal of the PpTEL1 C-terminus (including this third RRM) or only 16-18 amino acids within it seriously impairs PpTEL1 function, suggesting a critical role for this third RRM. These results show a conserved function of the RNA-binding PpTEL1 protein in the regulation of shoot development, from early ancestors to vascular plants, that depends on the third TEL-specific RRM.
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Affiliation(s)
- Julien Vivancos
- Institut de Biologie des Plantes-CNRS (UMR8618), Université Paris-Sud 11, Saclay Plant Sciences, 91405 Orsay Cedex, France
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15
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Lepers-Andrzejewski S, Siljak-Yakovlev S, Brown SC, Wong M, Dron M. Diversity and dynamics of plant genome size: an example of polysomaty from a cytogenetic study of Tahitian vanilla (Vanilla xtahitensis, Orchidaceae). Am J Bot 2011; 98:986-97. [PMID: 21613071 DOI: 10.3732/ajb.1000415] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/19/2023]
Abstract
PREMISE OF THE STUDY Abnormal mitotic behavior with somatic aneuploidy and partial endoreplication were previously reported for the first time in the plant kingdom in Vanilla planifolia. Because vanilla plants are vegetatively propagated, such abnormalities have been transmitted. This study aimed to determine whether mitotic abnormalities also occur in Vanilla hybrid or are suppressed by sexual reproduction. METHODS Twenty-eight accessions of Vanilla ×tahitensis, one V. planifolia, and hybrid V. planifolia × V. ×tahitensis were analyzed by chromosome counts, cytometry, and fluorescent in situ hybridization of 18S-5.8S-26S rDNA. KEY RESULTS In a single root meristem of V. ×tahitensis, chromosome number varied from 22 to 31 in diploids (mean 2C = 5.23 pg), 31 to 41 in triploids (2C = 7.82 pg) and 43 to 60 in tetraploids (2C = 10.27 pg). Morphological diversity is apparently related to ploidy changes. Aneuploidy and partial (asymmetrical) endoreduplication were observed in root meristems of both V. ×tahitensis and the hybrid V. planifolia × V. ×tahitensis, but pollen grains had the euploid chromosome number (n = 15 in diploids). CONCLUSIONS Genome irregularities may be transmitted not only during vegetative propagation but also by sexual reproduction in Vanilla. However, there must be a complex regulation of genome size and organization between the aneuploidy in somatic tissues and subsequently euploid gametic tissue. This is a novel example of polysomaty with developmentally regulated partial endoreplication.
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Affiliation(s)
- Sandra Lepers-Andrzejewski
- Etablissement Vanille de Tahiti, Département Recherche et Développement, BP 40135 Fare Tony 98713 Papeete, French Polynesia.
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16
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Dron M, Clouse SD, Dixon RA, Lawton MA, Lamb CJ. Glutathione and fungal elicitor regulation of a plant defense gene promoter in electroporated protoplasts. Proc Natl Acad Sci U S A 2010; 85:6738-42. [PMID: 16593981 PMCID: PMC282053 DOI: 10.1073/pnas.85.18.6738] [Citation(s) in RCA: 97] [Impact Index Per Article: 6.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
To investigate the mechanisms underlying activation of plant defenses against microbial attack we have studied elicitor regulation of a chimeric gene comprising the 5' flanking region of a defense gene encoding the phytoalexin biosynthetic enzyme chalcone synthase fused to a bacterial chloramphenicol acetyltransferase gene. Glutathione or fungal elicitor caused a rapid, marked but transient expression of the chimeric gene electroporated into soybean protoplasts. The response closely resembled that of endogenous chalcone synthase genes in suspension cultured cells. Functional analysis of 5' deletions suggests that promoter activity is determined by an elicitor-regulated activator located between the "TATA box" and nucleotide position -173 and an upstream silencer between -173 and -326. These cis-acting elements function in the transduction of the elicitation signal to initiate elaboration of an inducible defense response.
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Affiliation(s)
- M Dron
- Plant Biology Laboratory, Salk Institute for Biological Studies, P.O. Box 85800, San Diego, CA 92138
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17
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Dron M, Moudjou M, Chapuis J, Salamat MKF, Bernard J, Cronier S, Langevin C, Laude H. Endogenous proteolytic cleavage of disease-associated prion protein to produce C2 fragments is strongly cell- and tissue-dependent. J Biol Chem 2010; 285:10252-64. [PMID: 20154089 DOI: 10.1074/jbc.m109.083857] [Citation(s) in RCA: 50] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
The abnormally folded form of the prion protein (PrP(Sc)) accumulating in nervous and lymphoid tissues of prion-infected individuals can be naturally cleaved to generate a N-terminal-truncated fragment called C2. Information about the identity of the cellular proteases involved in this process and its possible role in prion biology has remained limited and controversial. We investigated PrP(Sc) N-terminal trimming in different cell lines and primary cultured nerve cells, and in the brain and spleen tissue from transgenic mice infected by ovine and mouse prions. We found the following: (i) the full-length to C2 ratio varies considerably depending on the infected cell or tissue. Thus, in primary neurons and brain tissue, PrP(Sc) accumulated predominantly as untrimmed species, whereas efficient trimming occurred in Rov and MovS cells, and in spleen tissue. (ii) Although C2 is generally considered to be the counterpart of the PrP(Sc) proteinase K-resistant core, the N termini of the fragments cleaved in vivo and in vitro can actually differ, as evidenced by a different reactivity toward the Pc248 anti-octarepeat antibody. (iii) In lysosome-impaired cells, the ratio of full-length versus C2 species dramatically increased, yet efficient prion propagation could occur. Moreover, cathepsin but not calpain inhibitors markedly inhibited C2 formation, and in vitro cleavage by cathepsins B and L produced PrP(Sc) fragments lacking the Pc248 epitope, strongly arguing for the primary involvement of acidic hydrolases of the endolysosomal compartment. These findings have implications on the molecular analysis of PrP(Sc) and cell pathogenesis of prion infection.
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Affiliation(s)
- Michel Dron
- INRA, U892 Virologie Immunologie Moléculaires, F-78350 Jouy-en-Josas, France
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18
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Charon C, Vivancos J, Mazubert C, Paquet N, Pilate G, Dron M. Structure and vascular tissue expression of duplicated TERMINAL EAR1-like paralogues in poplar. Planta 2010; 231:525-535. [PMID: 19943172 DOI: 10.1007/s00425-009-1066-4] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/04/2009] [Accepted: 10/23/2009] [Indexed: 05/28/2023]
Abstract
TERMINAL EAR1-like (TEL) genes encode putative RNA-binding proteins only found in land plants. Previous studies suggested that they may regulate tissue and organ initiation in Poaceae. Two TEL genes were identified in both Populus trichocarpa and the hybrid aspen Populus tremula x P. alba, named, respectively, PoptrTEL1-2 and PtaTEL1-2. The analysis of the organisation around the PoptrTEL genes in the P. trichocarpa genome and the estimation of the synonymous substitution rate for PtaTEL1-2 genes indicate that the paralogous link between these two Populus TEL genes probably results from the Salicoid large-scale gene-duplication event. Phylogenetic analyses confirmed their orthology link with the other TEL genes. The expression pattern of both PtaTEL genes appeared to be restricted to the mother cells of the plant body: leaf founder cells, leaf primordia, axillary buds and root differentiating tissues, as well as to mother cells of vascular tissues. Most interestingly, PtaTEL1-2 transcripts were found in differentiating cells of secondary xylem and phloem, but probably not in the cambium itself. Taken together, these results indicate specific expression of the TEL genes in differentiating cells controlling tissue and organ development in Populus (and other Angiosperm species).
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Affiliation(s)
- Céline Charon
- Institut de Biotechnologie des Plantes, CNRS (UMR8618), Université Paris-Sud 11, 91405 Orsay Cedex, France.
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Dron M, Dandoy-Dron F, Farooq Salamat MK, Laude H. Proteasome inhibitors promote the sequestration of PrPSc into aggresomes within the cytosol of prion-infected CAD neuronal cells. J Gen Virol 2009; 90:2050-2060. [PMID: 19339478 DOI: 10.1099/vir.0.010082-0] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Dysfunction of the endoplasmic reticulum associated protein degradation/proteasome system is believed to contribute to the initiation or aggravation of neurodegenerative disorders associated with protein misfolding, and there is some evidence to suggest that proteasome dysfunctions might be implicated in prion disease. This study investigated the effect of proteasome inhibitors on the biogenesis of both the cellular (PrP(C)) and abnormal (PrP(Sc)) forms of prion protein in CAD neuronal cells, a newly introduced prion cell system. In uninfected cells, proteasome impairment altered the intracellular distribution of PrP(C), leading to a strong accumulation in the Golgi apparatus. Moreover, a detergent-insoluble and weakly protease-resistant PrP species of 26 kDa, termed PrP(26K), accumulated in the cells, whether they were prion-infected or not. However, no evidence was found that, in infected cells, this PrP(26K) species converts into the highly proteinase K-resistant PrP(Sc). In the infected cultures, proteasome inhibition caused an increased intracellular aggregation of PrP(Sc) that was deposited into large aggresomes. These findings strengthen the view that, in neuronal cells expressing wild-type PrP(C) from the natural promoter, proteasomal impairment may affect both the process of PrP(C) biosynthesis and the subcellular sites of PrP(Sc) accumulation, despite the fact that these two effects could essentially be disconnected.
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Affiliation(s)
- Michel Dron
- INRA, U892 Virologie Immunologie Moléculaires, F-78350 Jouy-en-Josas, France
| | - Françoise Dandoy-Dron
- Centre National de la Recherche Scientifique, FRE2942, Oncologie Virale, F-94801 Villejuif, France
| | | | - Hubert Laude
- INRA, U892 Virologie Immunologie Moléculaires, F-78350 Jouy-en-Josas, France
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Geffroy V, Sévignac M, Billant P, Dron M, Langin T. Resistance to Colletotrichum lindemuthianum in Phaseolus vulgaris: a case study for mapping two independent genes. Theor Appl Genet 2008; 116:407-15. [PMID: 18060540 DOI: 10.1007/s00122-007-0678-y] [Citation(s) in RCA: 48] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/19/2007] [Accepted: 11/13/2007] [Indexed: 05/11/2023]
Abstract
Anthracnose, caused by the hemibiotrophic fungal pathogen Colletotrichum lindemuthianum is a devastating disease of common bean. Resistant cultivars are economical means for defense against this pathogen. In the present study, we mapped resistance specificities against 7 C. lindemuthianum strains of various geographical origins revealing differential reactions on BAT93 and JaloEEP558, two parents of a recombinant inbred lines (RILs) population, of Meso-american and Andean origin, respectively. Six strains revealed the segregation of two independent resistance genes. A specific numerical code calculating the LOD score in the case of two independent segregating genes (i.e. genes with duplicate effects) in a RILs population was developed in order to provide a recombination value (r) between each of the two resistance genes and the tested marker. We mapped two closely linked Andean resistance genes (Co-x, Co-w) at the end of linkage group (LG) B1 and mapped one Meso-american resistance genes (Co-u) at the end of LG B2. We also confirmed the complexity of the previously identified B4 resistance gene cluster, because four of the seven tested strains revealed a resistance specificity near Co-y from JaloEEP558 and two strains identified a resistance specificity near Co-9 from BAT93. Resistance genes found within the same cluster confer resistance to different strains of a single pathogen such as the two anthracnose specificities Co-x and Co-w clustered at the end of LG B1. Clustering of resistance specificities to multiple pathogens such as fungi (Co-u) and viruses (I) was also observed at the end of LG B2.
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Affiliation(s)
- Valérie Geffroy
- Institut de Biotechnologie des Plantes (IBP), INRA, Université Paris-Sud, UMR-CNRS 8618, bât. 630, 91405, Orsay Cedex, France.
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Klionsky DJ, Abeliovich H, Agostinis P, Agrawal DK, Aliev G, Askew DS, Baba M, Baehrecke EH, Bahr BA, Ballabio A, Bamber BA, Bassham DC, Bergamini E, Bi X, Biard-Piechaczyk M, Blum JS, Bredesen DE, Brodsky JL, Brumell JH, Brunk UT, Bursch W, Camougrand N, Cebollero E, Cecconi F, Chen Y, Chin LS, Choi A, Chu CT, Chung J, Clarke PGH, Clark RSB, Clarke SG, Clavé C, Cleveland JL, Codogno P, Colombo MI, Coto-Montes A, Cregg JM, Cuervo AM, Debnath J, Demarchi F, Dennis PB, Dennis PA, Deretic V, Devenish RJ, Di Sano F, Dice JF, Difiglia M, Dinesh-Kumar S, Distelhorst CW, Djavaheri-Mergny M, Dorsey FC, Dröge W, Dron M, Dunn WA, Duszenko M, Eissa NT, Elazar Z, Esclatine A, Eskelinen EL, Fésüs L, Finley KD, Fuentes JM, Fueyo J, Fujisaki K, Galliot B, Gao FB, Gewirtz DA, Gibson SB, Gohla A, Goldberg AL, Gonzalez R, González-Estévez C, Gorski S, Gottlieb RA, Häussinger D, He YW, Heidenreich K, Hill JA, Høyer-Hansen M, Hu X, Huang WP, Iwasaki A, Jäättelä M, Jackson WT, Jiang X, Jin S, Johansen T, Jung JU, Kadowaki M, Kang C, Kelekar A, Kessel DH, Kiel JAKW, Kim HP, Kimchi A, Kinsella TJ, Kiselyov K, Kitamoto K, Knecht E, Komatsu M, Kominami E, Kondo S, Kovács AL, Kroemer G, Kuan CY, Kumar R, Kundu M, Landry J, Laporte M, Le W, Lei HY, Lenardo MJ, Levine B, Lieberman A, Lim KL, Lin FC, Liou W, Liu LF, Lopez-Berestein G, López-Otín C, Lu B, Macleod KF, Malorni W, Martinet W, Matsuoka K, Mautner J, Meijer AJ, Meléndez A, Michels P, Miotto G, Mistiaen WP, Mizushima N, Mograbi B, Monastyrska I, Moore MN, Moreira PI, Moriyasu Y, Motyl T, Münz C, Murphy LO, Naqvi NI, Neufeld TP, Nishino I, Nixon RA, Noda T, Nürnberg B, Ogawa M, Oleinick NL, Olsen LJ, Ozpolat B, Paglin S, Palmer GE, Papassideri I, Parkes M, Perlmutter DH, Perry G, Piacentini M, Pinkas-Kramarski R, Prescott M, Proikas-Cezanne T, Raben N, Rami A, Reggiori F, Rohrer B, Rubinsztein DC, Ryan KM, Sadoshima J, Sakagami H, Sakai Y, Sandri M, Sasakawa C, Sass M, Schneider C, Seglen PO, Seleverstov O, Settleman J, Shacka JJ, Shapiro IM, Sibirny A, Silva-Zacarin ECM, Simon HU, Simone C, Simonsen A, Smith MA, Spanel-Borowski K, Srinivas V, Steeves M, Stenmark H, Stromhaug PE, Subauste CS, Sugimoto S, Sulzer D, Suzuki T, Swanson MS, Tabas I, Takeshita F, Talbot NJ, Tallóczy Z, Tanaka K, Tanaka K, Tanida I, Taylor GS, Taylor JP, Terman A, Tettamanti G, Thompson CB, Thumm M, Tolkovsky AM, Tooze SA, Truant R, Tumanovska LV, Uchiyama Y, Ueno T, Uzcátegui NL, van der Klei I, Vaquero EC, Vellai T, Vogel MW, Wang HG, Webster P, Wiley JW, Xi Z, Xiao G, Yahalom J, Yang JM, Yap G, Yin XM, Yoshimori T, Yu L, Yue Z, Yuzaki M, Zabirnyk O, Zheng X, Zhu X, Deter RL. Guidelines for the use and interpretation of assays for monitoring autophagy in higher eukaryotes. Autophagy 2008; 4:151-75. [PMID: 18188003 PMCID: PMC2654259 DOI: 10.4161/auto.5338] [Citation(s) in RCA: 1821] [Impact Index Per Article: 113.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023] Open
Abstract
Research in autophagy continues to accelerate,(1) and as a result many new scientists are entering the field. Accordingly, it is important to establish a standard set of criteria for monitoring macroautophagy in different organisms. Recent reviews have described the range of assays that have been used for this purpose.(2,3) There are many useful and convenient methods that can be used to monitor macroautophagy in yeast, but relatively few in other model systems, and there is much confusion regarding acceptable methods to measure macroautophagy in higher eukaryotes. A key point that needs to be emphasized is that there is a difference between measurements that monitor the numbers of autophagosomes versus those that measure flux through the autophagy pathway; thus, a block in macroautophagy that results in autophagosome accumulation needs to be differentiated from fully functional autophagy that includes delivery to, and degradation within, lysosomes (in most higher eukaryotes) or the vacuole (in plants and fungi). Here, we present a set of guidelines for the selection and interpretation of the methods that can be used by investigators who are attempting to examine macroautophagy and related processes, as well as by reviewers who need to provide realistic and reasonable critiques of papers that investigate these processes. This set of guidelines is not meant to be a formulaic set of rules, because the appropriate assays depend in part on the question being asked and the system being used. In addition, we emphasize that no individual assay is guaranteed to be the most appropriate one in every situation, and we strongly recommend the use of multiple assays to verify an autophagic response.
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Affiliation(s)
- Daniel J Klionsky
- Life Sciences Institute, University of Michigan, Ann Arbor, Michigan 48109-2216, USA.
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Dandoy-Dron F, Bogdanova A, Beringue V, Bailly Y, Tovey MG, Laude H, Dron M. Infection by ME7 prion is not modified in transgenic mice expressing the yeast chaperone Hsp104 in neurons. Neurosci Lett 2006; 405:181-5. [PMID: 16884849 DOI: 10.1016/j.neulet.2006.05.066] [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] [Received: 02/08/2006] [Revised: 05/08/2006] [Accepted: 05/29/2006] [Indexed: 10/24/2022]
Abstract
The Hsp104 chaperone induces thermo-tolerance in yeast and rescues proteins trapped in aggregates. In this study, we showed that xenogenic expression of Hsp104 dramatically increased the viability of the neuronal mouse CAD cell line after exposure to heat shock. These results indicate that the Hsp104 protein confers thermo-resistance to mammalian neuronal cells, the canonical property of Hsp104 in yeast. Hsp104 also determines the prion state of prion-like proteins in yeast and to investigate whether Hsp104 expression may modify mammalian prion infection in vivo, transgenic mice with specific expression of Hsp104 in neurons were generated. Mice develop and reproduce normally, they show no detectable physical defect and may constitute valuable model for the study of aggregation-prone neuropathological disorders. Hsp104 transgenic and control littermates were infected intracerebrally with the ME7 strain of scrapie. No differences in the incubation time of the disease or in PrP(Sc) accumulation were observed between transgenic and control mice. These results suggest that the heat-shock protein Hsp104 is not efficient to modulate the multiplication of mammalian prions and/or to counteract neurodegeneration in the brain of scrapie-infected mice.
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Affiliation(s)
- Françoise Dandoy-Dron
- CNRS UPR-9045, Laboratoire d'Oncologie Virale, 7 rue G. Môquet BP-8, 94801 Villejuif Cedex, France
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Dron M, Bailly Y, Beringue V, Haeberlé AM, Griffond B, Risold PY, Tovey MG, Laude H, Dandoy-Dron F. Scrg1 is induced in TSE and brain injuries, and associated with autophagy. Eur J Neurosci 2005; 22:133-46. [PMID: 16029203 DOI: 10.1111/j.1460-9568.2005.04172.x] [Citation(s) in RCA: 24] [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: 12/17/2022]
Abstract
We have previously identified Scrg1, a gene with increased cerebral mRNA levels in transmissible spongiform encephalopathies (TSE) such as scrapie, bovine spongiform encephalopathy and Creutzfeldt-Jakob disease. In this study, Scrg1-immunoreactive cells, essentially neurons, were shown to be widely distributed throughout the brain of scrapie-infected mice, while only rare and weakly immunoreactive cells could be detected in the brain of non-infected normal mice. Induction of the protein was confirmed by Western blot analysis. At the ultrastructural level, Scrg1 protein was associated with dictyosomes of the Golgi apparatus and autophagic vacuoles in the central neurons of the scrapie-infected mice. These results suggested a role for Scrg1 in the pathological changes observed in TSE. We have generated transgenic mice specifically expressing Scrg1 in neurons. No significant differences in the time course of the disease were detected between transgenic and non-transgenic mice infected with scrapie prions. However, tight association of Scrg1 with autophagic vacuoles was again observed in brain neurons of infected transgenic mice. High levels of the protein were also detected in degenerating Purkinje cells of Ngsk Prnp 0/0 mice overexpressing the Prnd gene coding for doppel, a neurotoxic paralogue of the prion protein. Furthermore, induction of Scrg1 protein was observed in the brain of mice injured by canine distemper virus or gold thioglucose treatment. Taken together, our results indicate that Scrg1 is associated with neurodegenerative processes in TSE, but is not directly linked to dysregulation of prion protein.
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Affiliation(s)
- Michel Dron
- CNRS UPR-9045, Laboratoire d'Oncologie Virale, 7 rue Guy Môquet BP-8, 94801 Villejuif Cedex, France
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Paquet N, Bernadet M, Morin H, Traas J, Dron M, Charon C. Expression patterns of TEL genes in Poaceae suggest a conserved association with cell differentiation. J Exp Bot 2005; 56:1605-1614. [PMID: 15837706 DOI: 10.1093/jxb/eri155] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/24/2023]
Abstract
Poaceae species present a conserved distichous phyllotaxy (leaf position along the stem) and share common properties with respect to leaf initiation. The goal of this work was to determine if these common traits imply common genes. Therefore, homologues of the maize TERMINAL EAR1 gene in Poaceae were studied. This gene encodes an RNA-binding motif (RRM) protein, that is suggested to regulate leaf initiation. Using degenerate primers, one unique tel (terminal ear1-like) gene from seven Poaceae members, covering almost all the phylogenetic tree of the family, was identified by PCR. These genes present a very high degree of similarity, a much conserved exon-intron structure, and the three RRMs and TEL characteristic motifs. The evolution of tel sequences in Poaceae strongly correlates with the known phylogenetic tree of this family. RT-PCR gene expression analyses show conserved tel expression in the shoot apex in all species, suggesting functional orthology between these genes. In addition, in situ hybridization experiments with specific antisense probes show tel transcript accumulation in all differentiating cells of the leaf, from the recruitment of leaf founder cells to leaf margins cells. Tel expression is not restricted to initiating leaves as it is also found in pro-vascular tissues, root meristems, and immature inflorescences. Therefore, these results suggest that TEL is not only associated with leaf initiation but more generally with cell differentiation in Poaceae.
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Affiliation(s)
- Nicolas Paquet
- Institut de Biotechnologie des Plantes (UMR8618), University of Paris XI, F-91405 Orsay Cedex, France
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Abstract
Scrapie responsive gene one (Scrg1) is a novel transcript discovered through identification of the genes associated with or responsible for the neurodegenerative changes observed in transmissible spongiform encephalopathies. Scrg1 mRNA is distributed principally in the central nervous system and the cDNA sequence predicts a small cysteine-rich protein 98 amino acids in length, with a N-terminal signal peptide. In this study, we have generated antibodies against the predicted protein and revealed expression of a predominant immunoreactive protein of 10 kDa in mouse brain by Western blot analysis. We have established CAD neuronal cell lines stably expressing Scrg1 to determine its subcellular localization. Several lines of evidence show that the protein is targeted to dense-core vesicles in these cells. (i) Scrg1 is detected by immunocytochemistry as very punctate signals especially in the Golgi apparatus and tips of neurites, suggesting a vesicular localization for the protein. Moreover, Scrg1 exhibits a high degree of colocalization with secretogranin II, a dense-core vesicle marker and a very limited colocalization with markers for small synaptic vesicles. (ii) Scrg1 immunoreactivity is associated with large secretory granules/dense-core vesicles, as indicated by immuno-electron microscopy. (iii) Scrg1 is enriched in fractions of sucrose density gradient where synaptotagmin V, a dense-core vesicle-associated protein, is also enriched. The characteristic punctate immunostaining of Scrg1 is observed in N2A cells transfected with Scrg1 and for the endogenous protein in cultured primary neurons, attesting to the generality of the observations. Our findings strongly suggest that Scrg1 is associated with the secretory pathway of neuronal cells.
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Affiliation(s)
- Françoise Dandoy-Dron
- Laboratoire d'Oncologie Virale, CNRS UPR 9045, 7 rue G. Môquet BP-8, 94801 Villejuif Cedex, France
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Dron M, Meritet JF, Dandoy-Dron F, Meyniel JP, Maury C, Tovey MG. Molecular cloning of ADIR, a novel interferon responsive gene encoding a protein related to the torsins. Genomics 2002; 79:315-25. [PMID: 11863361 DOI: 10.1006/geno.2002.6709] [Citation(s) in RCA: 29] [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: 11/22/2022]
Abstract
The expression of the previously uncharacterized gene Adir (for ATP dependent interferon responsive gene) was increased by 5- to 15-fold in tissue of the oral cavity or in spleen and liver of mice treated orally or intraperitoneally with IFN-alpha, and in mouse cells treated in vitro with IFN-alpha or IFN-gamma. The level of Adir mRNA was also increased 20- to 40-fold in the brains of animals infected with encephalomyocarditis virus. Adir is expressed ubiquitously in mouse tissues as 1.9-, 2.4-, and 3.5-kb mRNA transcripts encoding a 385-amino-acid protein with a conserved ATP binding domain containing typical nucleotide and Mg(2+) binding sites. We also characterized the human ortholog, ADIR, which is located on chromosome 1q25-q31 and contains six exons encoding a 397-amino-acid protein with 80% homology to the mouse protein. A single 2.3-kb mRNA was detected in all human tissues examined, except for placenta, which also contained a 1.25-kb tissue-specific transcript generated by alternative splicing and encoding a putative 336-amino-acid protein. Although ADIR exhibits low homology to DYT1 and TOR1B, the deduced ADIR protein sequences are highly homologous to torsin A and torsin B and more distantly related to members of the Clp/HSP100 family of proteins, suggesting that ADIR, like torsins, is related to the AAA chaperone-like family of ATPases. An ADIR-EGFP fusion protein expressed in HeLa cells was shown to be associated with the endoplasmic reticulum.
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Affiliation(s)
- Michel Dron
- Laboratory of Viral Oncology CNRS UPR 9045, Institute André Lwoff, Villejuif Cedex, 94801, France
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27
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Dron M, Tartare X, Guillo F, Haik S, Barbin G, Maury C, Tovey M, Dandoy-Dron F. Mouse scrapie responsive gene 1 (Scrg1): genomic organization, physical linkage to sap30, genetic mapping on chromosome 8, and expression in neuronal primary cell cultures. Genomics 2000; 70:140-9. [PMID: 11087671 DOI: 10.1006/geno.2000.6358] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.5] [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: 11/22/2022]
Abstract
We have previously reported a transcript of a novel mouse gene (Scrg1) with increased expression in transmissible spongiform encephalopathies and the cloning of the human mRNA analogue. In this paper, we present the genomic organization of the mouse and human SCRG1 loci, which exhibit a high degree of conservation. The genes are composed of three exons; the two downstream exons contain the protein coding region. The mouse gene is expressed in brain tissue essentially as a 0.7-kb message but also as a minor 2.6-kb mRNA. We have sequenced 20 kb of DNA at the mouse Scrg1 locus and found that the longer transcript is the prolongation of the 0.7-kb mRNA to a polyadenylation site located about 2 kb further downstream. Sequencing revealed that the mouse Scrg1 gene is physically linked to Sap30, a gene that encodes a protein of the histone deacetylase complex, and genetic linkage mapping assigned the localization of Scrg1 to chromosome 8 between Ant1 and Hmg2. Northern blot analysis showed that Scrg1 is under strict developmental control in mouse embryo and is expressed by cells of neuronal origin in vitro. Comparison of the rat, mouse, and human SCRG1 proteins identified a box of 35 identical contiguous amino acids and a characteristic cysteine distribution pattern defining a new protein signature.
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Affiliation(s)
- M Dron
- Laboratory of Viral Oncology, CNRS UPR 9045, Villejuif Cedex, 94801, France
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29
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Dandoy-Dron F, Benboudjema L, Guillo F, Jaegly A, Jasmin C, Dormont D, Tovey MG, Dron M. Enhanced levels of scrapie responsive gene mRNA in BSE-infected mouse brain. Brain Res Mol Brain Res 2000; 76:173-9. [PMID: 10719228 DOI: 10.1016/s0169-328x(00)00028-0] [Citation(s) in RCA: 29] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
The expression of the mRNA of nine scrapie responsive genes was analyzed in the brains of FVB/N mice infected with bovine spongiform encephalopathy (BSE). The RNA transcripts of eight genes were overexpressed to a comparable extent in both BSE-infected and scrapie-infected mice, indicating a common series of pathogenic events in the two transmissible spongiform encephalopathies (TSEs). In contrast, the serine proteinase inhibitor spi 2, an analogue of the human alpha-1 antichymotrypsin gene, was overexpressed to a greater extent in the brains of scrapie-infected animals than in animals infected with BSE, reflecting either an agent specific or a mouse strain specific response. The levels of spi 2 mRNA were increased during the course of scrapie prior to the onset of clinical signs of the disease and the increase reached 11 to 45 fold relative to uninfected controls in terminally ill mice. Spi 2, in common with four of the other scrapie responsive genes studied, is known to be associated with pro-inflammatory processes. These observations underline the importance of cell reactivity in TSE. In addition, scrg2 mRNA the level of which is enhanced in TSE-infected mouse brain, was identified as a previously unrecognized long transcript of the murine aldolase C gene. However, the level of the principal aldolase C mRNA is unaffected in TSE. The increased representation of the longer transcript in the late stage of the disease may reflect changes in mRNA processing and/or stability in reactive astrocytes or in damaged Purkinje cells.
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Affiliation(s)
- F Dandoy-Dron
- Laboratoire d'Oncologie Virale, CNRS UPR 9045, 7 rue guy Moquet, BP8, IFC1, 94801, Villejuif cedex, France
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Geffroy V, Sévignac M, De Oliveira JC, Fouilloux G, Skroch P, Thoquet P, Gepts P, Langin T, Dron M. Inheritance of partial resistance against Colletotrichum lindemuthianum in Phaseolus vulgaris and co-localization of quantitative trait loci with genes involved in specific resistance. Mol Plant Microbe Interact 2000; 13:287-96. [PMID: 10707354 DOI: 10.1094/mpmi.2000.13.3.287] [Citation(s) in RCA: 62] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/19/2023]
Abstract
Anthracnose, one of the most important diseases of common bean (Phaseolus vulgaris), is caused by the fungus Colletotrichum lindemuthianum. A "candidate gene" approach was used to map anthracnose resistance quantitative trait loci (QTL). Candidate genes included genes for both pathogen recognition (resistance genes and resistance gene analogs [RGAs]) and general plant defense (defense response genes). Two strains of C. lindemuthianum, identified in a world collection of 177 strains, displayed a reproducible and differential aggressiveness toward BAT93 and JaloEEP558, two parental lines of P. vulgaris representing the two major gene pools of this crop. A reliable test was developed to score partial resistance in aerial organs of the plant (stem, leaf, petiole) under controlled growth chamber conditions. BAT93 was more resistant than JaloEEP558 regardless of the organ or strain tested. With a recombinant inbred line (RIL) population derived from a cross between these two parental lines, 10 QTL were located on a genetic map harboring 143 markers, including known defense response genes, anthracnose-specific resistance genes, and RGAs. Eight of the QTL displayed isolate specificity. Two were co-localized with known defense genes (phenylalanine ammonia-lyase and hydroxyproline-rich glycoprotein) and three with anthracnose-specific resistance genes and/or RGAs. Interestingly, two QTL, with different allelic contribution, mapped on linkage group B4 in a 5.0 cM interval containing Andean and Mesoamerican specific resistance genes against C. lindemuthianum and 11 polymorphic fragments revealed with a RGA probe. The possible relationship between genes underlying specific and partial resistance is discussed.
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Affiliation(s)
- V Geffroy
- LPPM, IBP, Université de Paris XI, Orsay, France.
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31
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Geffroy V, Sicard D, de Oliveira JC, Sévignac M, Cohen S, Gepts P, Neema C, Langin T, Dron M. Identification of an ancestral resistance gene cluster involved in the coevolution process between Phaseolus vulgaris and its fungal pathogen Colletotrichum lindemuthianum. Mol Plant Microbe Interact 1999; 12:774-84. [PMID: 10494630 DOI: 10.1094/mpmi.1999.12.9.774] [Citation(s) in RCA: 38] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/03/2023]
Abstract
The recent cloning of plant resistance (R) genes and the sequencing of resistance gene clusters have shed light on the molecular evolution of R genes. However, up to now, no attempt has been made to correlate this molecular evolution with the host-pathogen coevolution process at the population level. Cross-inoculations were carried out between 26 strains of the fungal pathogen Colletotrichum lindemuthianum and 48 Phaseolus vulgaris plants collected in the three centers of diversity of the host species. A high level of diversity for resistance against the pathogen was revealed. Most of the resistance specificities were overcome in sympatric situations, indicating an adaptation of the pathogen to the local host. In contrast, plants were generally resistant to allopatric strains, suggesting that R genes that were efficient against exotic strains but had been overcome locally were maintained in the plant genome. These results indicated that coevolution processes between the two protagonists led to a differentiation for resistance in the three centers of diversity of the host. To improve our understanding of the molecular evolution of these different specificities, a recombinant inbred (RI) population derived from two representative genotypes of the Andean (JaloEEP558) and Mesoamerican (BAT93) gene pools was used to map anthracnose specificities. A gene cluster comprising both Andean (Co-y; Co-z) and Mesoamerican (Co-9) host resistance specificities was identified, suggesting that this locus existed prior to the separation of the two major gene pools of P. vulgaris. Molecular analysis revealed a high level of complexity at this locus. It harbors 11 restriction fragment length polymorphisms when R gene analog (RGA) clones are used. The relationship between the coevolution process and diversification of resistance specificities at resistance gene clusters is discussed.
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Affiliation(s)
- V Geffroy
- IBP-LPPM, Université de Paris XI, Orsay, France.
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32
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Creusot F, Macadré C, Ferrier Cana E, Riou C, Geffroy V, Sévignac M, Dron M, Langin T. Cloning and molecular characterization of three members of the NBS-LRR subfamily located in the vicinity of the Co-2 locus for anthracnose resistance in Phaseolus vulgaris. Genome 1999; 42:254-64. [PMID: 10231959 DOI: 10.1139/g98-134] [Citation(s) in RCA: 24] [Impact Index Per Article: 1.0] [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: 11/22/2022]
Abstract
Co-2 is one of the R-genes against anthracnose identified in common bean. A RAPD marker, cloned as PvH20, was previously shown to contain 6 imperfect leucine-rich-repeats and to reveal a family of related sequences in the vicinity of the Co-2 locus. Using PvH20 as probe, a genomic clone and 2 partial cDNAs were isolated. DNA sequencing revealed that the 6.1 kb genomic fragment contains sequences encoding both NBS-LRR (ORF1) and kinase-like (ORF2) products. The 2 partial cDNAs (cD7 and cD8) belong to the NBS-LRR subfamily as do most of the resistance genes cloned to date. The LRR domain of ORF1 is interrupted by 2 stop codons suggesting that it corresponds to a non-functional member of the multigene family and ORF2 appears to be a kinase pseudogene. The 3 NBS-LRR polypeptides share a high level of amino acid identity and represent different members of a related family. By genetic mapping ORF1, cD7, and cD8 were found to span a genetic distance of 3 cM: cD8 maps at 2 cM from Co-2 and 3 cM from ORF1, cD7 maps at 1 cM from ORF1 and co-segregates with Co-2, thus cD7 might be a putative candidate for the Co-2 R-gene.
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Affiliation(s)
- F Creusot
- Université Paris-Sud, CNRS UMR 8618, ORSAY, France.
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Dron M, Hameau L, Benboudjema L, Guymarho J, Cajean-Feroldi C, Rizza P, Godard C, Jasmin C, Tovey MG, Lang MC. Cloning of a long HIV-1 readthrough transcript and detection of an increased level of early growth response protein-1 (Egr-1) mRNA in chronically infected U937 cells. Arch Virol 1999; 144:19-28. [PMID: 10076506 DOI: 10.1007/s007050050482] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.3] [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: 10/28/2022]
Abstract
To identify the pathways involved in HIV-1 modification of cellular gene expression, chronically infected U937 cells were screened by mRNA differential display. A chimeric transcript consisting of the 3' end of the LTR of a HIV-1 provirus, followed by 3.7 kb of cellular RNA was identified suggesting that long readthrough transcription might be one of the mechanisms by which gene expression could be modified in individual infected cells. Such a phenomenon may also be the first step towards the potential transduction of cellular sequences. Furthermore, the mRNA encoding for the transcription factor Egr-1 was detected as an over-represented transcript in infected cells. Northern blot analysis confirmed the increase of Egr-1 mRNA content in both HIV-1 infected promonocytic U937 cells and T cell lines such as Jurkat and CEM. Interestingly a similar increase of Egr-1 mRNA has previously been reported to occur in HTLV-1 and HTLV-2 infected T cell lines. Despite the consistent increase in the level of Egr-1 mRNA, the amount of the encoded protein did not appear to be modified in HIV-1 infected cells, suggesting an increased turn over of the protein in chronically infected cells.
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Affiliation(s)
- M Dron
- Laboratory of Viral Oncology, C.N.R.S., Villejuif, France
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Creusot F, Macadré C, Cana EF, Riou C, Geffroy V, Sévignac M, Dron M, Langin T. Cloning and molecular characterization of three members of the NBS-LRR subfamily located in the vicinity of the Co-2 locus for anthracnose resistance in Phaseolus vulgaris. Genome 1999. [DOI: 10.1139/gen-42-2-254] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
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Dron M, Dandoy-Dron F, Guillo F, Benboudjema L, Hauw JJ, Lebon P, Dormont D, Tovey MG. Characterization of the human analogue of a Scrapie-responsive gene. J Biol Chem 1998; 273:18015-8. [PMID: 9660755 DOI: 10.1074/jbc.273.29.18015] [Citation(s) in RCA: 20] [Impact Index Per Article: 0.8] [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
We have recently described a novel mRNA denominated ScRG-1, the level of which is increased in the brains of Scrapie-infected mice (Dandoy-Dron, F., Guillo, F., Benboudjema, L., Deslys, J.-P., Lasmézas, C., Dormont, D., Tovey, M. G., and Dron, M. (1998) J. Biol. Chem. 273, 7691-7697). The increase in ScRG-1 mRNA in the brain follows the accumulation of PrPSc, the proteinase K-resistant form of the prion protein (PrP), and precedes the widespread neuronal death that occurs in late stage disease. In the present study, we have isolated a cDNA encoding the human counterpart of ScRG-1. Comparison of the human and mouse transcripts firmly established that both sequences encode a highly conserved protein of 98 amino acids that contains a signal peptide, suggesting that the protein may be secreted. Examination of the distribution of human ScRG-1 mRNA in adult and fetal tissues revealed that the gene was expressed primarily in the central nervous system as a 0.7-kilobase message and was under strict developmental control.
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Affiliation(s)
- M Dron
- Laboratory of Viral Oncology CNRS UPR 9045, IFC1, 94801 Villejuif cedex, France.
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36
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Abstract
Higher plants contain a multigene family encoding proteins that share a highly conserved catalytic protein kinase domain about 70% identical to SHAGGY protein kinase (SGG) and glycogen synthase kinase-3 (GSK-3), respectively, from Drosophila and mammals. In this study we have characterized the structure and evolution of the Arabidopsis SHAGGY-related protein kinase (ASK) gene family. At least ten ASK genes are present per haploid genome of Arabidopsis. The genomic sequences of five ASK genes show a strikingly high conservation of intron positions and exon lengths. Phylogenetic analyses suggested that the Arabidopsis gene family contains at least three ancient classes of genes that diverged early in land plant evolution. The different classes may reflect specificity of substrates and/or biological functions. Eight out of the ten predicted ASK genes were mapped and shown to be dispersed over the five Arabidopsis chromosomes. A tentative model for the organization and evolution of the Arabidopsis ASK genes is presented.
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Affiliation(s)
- M C Dornelas
- Institut de Biotechnologie des Plantes, ERS/CNRS 569, Université de Paris-Sud, Bâtiment 630, F-91405, Orsay, Cedex, France
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O'Sullivan D, Tosi P, Creusot F, Cooke BM, Phan TH, Dron M, Langin T. Variation in genome organization of the plant pathogenic fungus Colletotrichum lindemuthianum. Curr Genet 1998; 33:291-8. [PMID: 9560437 DOI: 10.1007/s002940050339] [Citation(s) in RCA: 29] [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: 02/07/2023]
Abstract
The genome structure of Colletotrichum lindemuthianum in a set of diverse isolates was investigated using a combination of physical and molecular approaches. Flow cytometric measurement of genome size revealed significant variation between strains, with the smallest genome representing 59% of the largest. Southern-blot profiles of a cloned fungal telomere revealed a total chromosome number varying from 9 to 12. Chromosome separations using pulsed-field gel electrophoresis (PFGE) showed that these chromosomes belong to two distinct size classes: a variable number of small (< 2.5 Mb) polymorphic chromosomes and a set of unresolved chromosomes larger than 7 Mb. Two dispersed repeat elements were shown to cluster on distinct polymorphic minichromosomes. Single-copy flanking sequences from these repeat-containing clones specifically marked distinct small chromosomes. These markers were absent in some strains, indicating that part of the observed variability in genome organization may be explained by the presence or absence, in a given strain, of dispensable genomic regions and/or chromosomes.
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Affiliation(s)
- D O'Sullivan
- Institut de Biotechnologie des Plantes, Université de Paris-Sud, Cedex, France
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Dandoy-Dron F, Guillo F, Benboudjema L, Deslys JP, Lasmézas C, Dormont D, Tovey MG, Dron M. Gene expression in scrapie. Cloning of a new scrapie-responsive gene and the identification of increased levels of seven other mRNA transcripts. J Biol Chem 1998; 273:7691-7. [PMID: 9516475 DOI: 10.1074/jbc.273.13.7691] [Citation(s) in RCA: 105] [Impact Index Per Article: 4.0] [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
To define genes associated with or responsible for the neurodegenerative changes observed in transmissible spongiform encephalopathies, we analyzed gene expression in scrapie-infected mouse brain using "mRNA differential display." The RNA transcripts of eight genes were increased 3-8-fold in the brains of scrapie-infected animals. Five of these genes have not previously been reported to exhibit increased expression in this disease: cathepsin S, the C1q B-chain of complement, apolipoprotein D, and two previously unidentified genes denominated scrapie-responsive gene (ScRG)-1 and ScRG-2, which are preferentially expressed in brain tissue. Increased expression of the three remaining genes, beta2 microglobulin, F4/80, and metallothionein II, has previously been reported to occur in experimental scrapie. Kinetic analysis revealed a concomitant increase in the levels of ScRG-1, cathepsin S, the C1q B-chain of complement, and beta2 microglobulin mRNA as well as glial fibrillary acidic protein and F4/80 transcripts, markers of astrocytosis and microglial activation, respectively. In contrast, the level of ScRG-2, apolipoprotein D, and metallothionein II mRNA was only increased at the terminal stage of the disease. ScRG-1 mRNA was found to be preferentially expressed in glial cells and to code for a short protein of 47 amino acids with a strong hydrophobic N-terminal region.
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Affiliation(s)
- F Dandoy-Dron
- Laboratoire d'Oncologie Virale CNRS UPR 9045, IFC1, 94801 Villejuif cedex France
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Geffroy V, Creusot F, Falquet J, Sévignac M, Adam-Blondon AF, Bannerot H, Gepts P, Dron M. A family of LRR sequences in the vicinity of the Co-2 locus for anthracnose resistance in Phaseolus vulgaris and its potential use in marker-assisted selection. Theor Appl Genet 1998; 96:494-502. [PMID: 24710889 DOI: 10.1007/s001220050766] [Citation(s) in RCA: 35] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/11/2023]
Abstract
Molecular markers offer new opportunities for breeding for disease resistance. Resistance gene pyramiding in a single cultivar, as a strategy for durable resistance, can be facilitated by marker-assisted selection (MAS). A RAPD marker, ROH20(450), linked to the Mesoamerican Co-2 anthracnose resistance gene, was previously transformed into a SCAR marker, SCH20. In the present paper we have further characterized the relevance of the SCH20 SCAR marker in different genetic backgrounds. Since this SCAR marker was found to be useful mainly in the Andean gene pool, we identified a new PCR-based marker (SCAreoli) for indirect scoring of the presence of the Co-2 gene. The SCAreoli SCAR marker is polymorphic in the Mesoamerican as well as in the Andean gene pool and should be useful in MAS. We also report that PvH20, the cloned sequence corresponding to the 450-bp RAPD marker ROH20(450), contains six imperfect leucine-rich repeats, and reveals a family of related sequences in the vicinity of the Co-2 locus. These results are discussed in the context of the recent cloning of some plant resistance genes.
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Affiliation(s)
- V Geffroy
- LPPM, IBP, Bât, 630, Université Paris Sud, 91405 ORSAY Cedex, France E-mail: , FR
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Dufresne M, Bailey JA, Dron M, Langin T. clk1, a serine/threonine protein kinase-encoding gene, is involved in pathogenicity of Colletotrichum lindemuthianum on common bean. Mol Plant Microbe Interact 1998; 11:99-108. [PMID: 9450334 DOI: 10.1094/mpmi.1998.11.2.99] [Citation(s) in RCA: 57] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/22/2023]
Abstract
A random insertional mutagenesis in Colletotrichum lindemuthianum, the causal agent of common bean anthracnose, generated four mutants that showed altered pathogenicity when tested on intact seedlings, excised leaves, and/or excised hypocotyls. One of these mutants, H290, produced very few lesions on bean leaves and appeared affected in its ability to penetrate the leaf cuticle. Molecular analyses showed that the border sequences of the unique integration site of the disrupting pAN7-1 plasmid in the mutant exhibited homology with conserved domains of serine/threonine protein kinases. The corresponding wild-type sequences were cloned and a gene replacement vector with a mutated copy harboring a selection marker constructed. Transformation of the wild-type pathogen produced a strain with a phenotype identical to the original mutant. Genomic and cDNA sequences indicated that the disrupted gene is a member of the serine/threonine protein kinase family. The gene, called clk1 (Colletotrichum lindemuthianum kinase 1), was weakly expressed in the mycelium of the wild-type strain grown on rich and minimal synthetic media but was undetectable during the infection even when a sensitive reverse transcriptase-polymerase chain reaction methodology was used. This study represents the first characterization of altered pathogenicity mutants in C. lindemuthianum produced by random mutagenesis and demonstrates the involvement of a member of the serine/threonine kinase gene family in the early steps of the infection process.
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Affiliation(s)
- M Dufresne
- Laboratoire de Phytopathologie Moléculaire, Université Paris-Sud, Orsay, France.
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Sicard D, Michalakis Y, Dron M, Neema C. Genetic Diversity and Pathogenic Variation of Colletotrichum lindemuthianum in the Three Centers of Diversity of Its Host, Phaseolus vulgaris. Phytopathology 1997; 87:807-13. [PMID: 18945048 DOI: 10.1094/phyto.1997.87.8.807] [Citation(s) in RCA: 27] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/15/2023]
Abstract
ABSTRACT Population subdivision of Colletotrichum lindemuthianum, the causal agent of anthracnose, was studied in three regions located in three centers of diversity of its host, Phaseolus vulgaris. Random amplified polymorphic DNA (RAPD) markers, restriction endonuclease analysis of the amplified ribosomal internal transcribed spacer region, and virulence on a set of 12 cultivars were used to assess the genetic diversity of C. lindemuthianum strains isolated in Mexican, Ecuadorian, and Argentinean wild common bean populations. The three regions were significantly differentiated for molecular markers. For these markers, Mexico was the most polymorphic and the most distant from Ecuador and Argentina. The majority of the RAPD alleles present in Ecuador and Argentina were found in Mexico, suggesting that Andean populations have been derived from the Mesoamerican center. Pathogenicity tests on a set of 12 cultivars showed that all but one of the Mexican strains were virulent exclusively on Mesoamerican cultivars. Argentinean strains were virulent preferentially on southern Andes cultivars, and the Ecuadorian strains, except for one strain, were avirulent on all cultivars. These results suggest an adaptation of strains on cultivars of the same geographic origin. Thus, based on molecular and virulence markers, C. lindemuthianum strains isolated from wild common bean populations were divided into three groups corresponding to host gene pools.
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Dron M, Manuelidis L. Visualization of viral candidate cDNAs in infectious brain fractions from Creutzfeldt-Jakob disease by representational difference analysis. J Neurovirol 1996; 2:240-8. [PMID: 8799215 DOI: 10.3109/13550289609146887] [Citation(s) in RCA: 18] [Impact Index Per Article: 0.6] [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] [Indexed: 02/02/2023]
Abstract
Creutzfeldt-Jakob Disease (CJD), a neurodegenerative and dementing disease of later life, is caused by a viruslike entity that is incompletely characterized. As in scrapie, all more purified infectious brain preparations contain nucleic acids. However, it has not been possible to visualize unique bands that may derive from a viral genome. We here used a subtractive strategy known as representational difference analysis (RDA) to uncover such sequences. To reduce the complexity of starting target nucleic acids, sucrose gradients were first used to select nuclease resistant particles with a defined 120S size. In CJD this single 120S gradient peak is highly enriched for infectivity, and contains reduced amounts of PrP (Proc. Natl. Acad. Sci. 92, 5124-8, 1995). Parallel 120S fractions from uninfected brain were made to generate subtractor sequences. 120S particles were lysed in GdnSCN, and ng amounts of released RNA were purified for random-primed cDNA synthesis. To capture representative fragments of 100-500 bp, cDNAs were cleaved with Mbo I for adaptor ligation and amplification. In the first experiment with moderate RDA selection, it was possible to visualize clones from CJD cDNA that did not hybridize to control cDNA. In the second experiment, more exhaustive subtractions yielded a discrete set of CJD derived gel bands. Competitive hybridization showed a subset of these bands were not present in either the control 120S cDNA or in the hamster genome. This represents the first demonstration of apparently CJD-specific nucleic acid bands in more purified infectious preparations. Although exhaustive cloning, sequencing and correlative titration studies need to be done, it is encouraging that most of the viral candidates selected thus far have no significant homology with any previously described sequence in the database.
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Affiliation(s)
- M Dron
- Yale Medical School, New Haven, Connecticut 06510, USA
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Creusot F, Fouilloux E, Dron M, Lafleuriel J, Picard G, Billault A, Le Paslier D, Cohen D, Chabouté ME, Durr A. The CIC library: a large insert YAC library for genome mapping in Arabidopsis thaliana. Plant J 1995; 8:763-770. [PMID: 8528287 DOI: 10.1046/j.1365-313x.1995.08050763.x] [Citation(s) in RCA: 81] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/22/2023]
Abstract
A new Arabidopsis thaliana (ecotype Columbia) genomic library has been constructed in Yeast Artificial Chromosomes: the CIC library (for CEPH, INRA and CNRS). Optimization of plant culture conditions and protoplast preparation allowed the recovery of large amounts of viable protoplasts. Mechanical shearing of DNA was minimized by isolation of DNA from protoplasts embedded in agarose. Cloning of large inserts was favored by including two successive size fractionation steps (after partial EcoRI digestion and after ligation with the vector arms), which selected DNA fragments larger than 350 kb. The library consists of 1152 clones with an average insert size of 420 kb. Clones carrying chloroplast DNA and various nuclear repeated sequences have been identified. Twenty-one per cent of the clones are found to contain chloroplast DNA. Therefore, the library represents around four nuclear genome equivalents. The clones containing 5S rDNA genes, 18S-25S rDNA sequences and the 180 bp paracentromeric repeated element account for 3.6%, 8.9% and 5.8%, respectively. Only one clone was found to carry the 160 bp paracentromeric repeated element. Given the smaller size of clones carrying Arabidopsis repeated DNA, the average size of remaining clones is around 480 kb. The library was screened by PCR amplification using pairs of primers corresponding to sequences dispersed in the genome. Seventy out of 76 pairs of primers identified from one to seven YAC clones. Thus at least 92% of the genome is represented in the CIC library. The survey of the library for clones containing unlinked DNA sequences indicates that the proportion of chimeric clones is lower than 10%.
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Affiliation(s)
- F Creusot
- Laboratoire de Phytopathologie Moléculaire, URA CNRS 1128, Université Paris-sud, Orsay, France
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Fabre J, Julien J, Parisot D, Dron M. Analysis of diverse isolates of Colletotrichum lindemuthianum infecting common bean using molecular markers. ACTA ACUST UNITED AC 1995. [DOI: 10.1016/s0953-7562(09)80640-0] [Citation(s) in RCA: 23] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/21/2022]
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Abstract
A bean genetic map was developed to locate resistance genes against anthracnose and genes involved in plant defense mechanisms. One hundred and fifty-seven markers (51 restriction fragment length polymorphism, 100 random amplified polymorphic DNA, 2 sequence characterized amplified regions, and 4 morphological markers) were used to construct a genetic map covering 567.5 cM of the bean genome. Morphological markers consisted in two resistance genes towards anthracnose (Are and RVI), a dominant gene for nuclear male sterility (Ms8) and a pod-shape character (SGou). This map was established by using a backcross population (BC1) of 128 individuals, derived from a cross between two European bean genotypes: Ms8EO2 and Corel. Nine percent of the markers showed segregation distortions and mapped to three regions. Clusters of 2-10 markers were observed in every linkage group. The possible origin of these clusters is discussed. Nineteen markers shared with a previously published bean linkage map allowed us to establish a preliminary correspondence between the two maps. Finally, seven genes involved in plant defense mechanisms were located on this map.
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Affiliation(s)
- A F Adam-Blondon
- Département de Biologie Moléculaire Végétale, Université Paris-Sud, Orsay, France
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Adam-Blondon AF, Sévignac M, Bannerot H, Dron M. SCAR, RAPD and RFLP markers linked to a dominant gene (Are) conferring resistance to anthracnose in common bean. Theor Appl Genet 1994; 88:865-70. [PMID: 24186190 DOI: 10.1007/bf01253998] [Citation(s) in RCA: 32] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/13/1993] [Accepted: 12/21/1993] [Indexed: 05/20/2023]
Abstract
Anthracnose, caused by the fungusColletotrichum lindemuthianum, is a severe disease of common bean (Phaseolus vulgaris L.) controlled, in Europe, by a single dominant gene,Are. Four pairs of near-isogenic lines (NILs) were constructed, in which theAre gene was introgressed into different genetic backgrounds. These pairs of NILs were used to search for DNA markers linked to the resistance gene. Nine molecular markers, five RAPDs and four RFLPs, were found to discriminate between the resistant and the susceptible members of these NILs. A backcross progeny of 120 individuals was analysed to map these markers in relation to theAre locus. Five out of the nine markers were shown to be linked to theAre gene within a distance of 12.0 cM. The most tightly linked, a RAPD marker, was used to generate a pair of primers that specifically amplify this RAPD (sequence characterized amplified region, SCAR).
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Affiliation(s)
- A F Adam-Blondon
- Dépt Biol Mol Végétale, Bat 430, Université Paris Sud, 91405, Orsay Cedex, France
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Gantet P, Bettini P, Dron M. Light and developmental regulation of the Anp-controlled anthocyanin phenotype of bean pods. Theor Appl Genet 1993; 87:1-8. [PMID: 24190183 DOI: 10.1007/bf00223735] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/20/1993] [Accepted: 03/29/1993] [Indexed: 06/02/2023]
Abstract
In the presence of the dominant allele of the Anp gene, bean pods present a purple-mottled phenotype. The purple pigmentation is variable from cell to cell in the pod epidermal layer and develops as a random mosaic. Three anthocyanidins, delphinidin, petunidin and malvidin, are involved in this purple pigmentation. Anthocyanins accumulated in vacuoles; anthocyanoplasts and cristal bodies were also observed occasionally. A developmental switch is a prerequisite for anthocyanin accumulation in the pods. This does not occur before day 4 after pollination and is controlled by light in competent pods. mRNAs for PAL, CHS, CHI, DFR and UFGT are induced in the pods, indicating that the general anthocyanin biosynthetic pathway is well conserved at both the biochemical and molecular levels in this species. mRNA steady-state level studies of PAL and CHS suggest that the light regulation occurs at the transcriptional level.
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Affiliation(s)
- P Gantet
- Department of Plant Molecular Biology, URA CNRS 1128, Bât. 430, Université Paris XI, 91405, Orsay cedex, France
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Dron M, Tovey MG. Interferon-resistant Daudi cells are deficient in interferon-alpha-induced ISGF3 alpha activation, but remain sensitive to the interferon-alpha-induced increase in ISGF3 gamma content. J Interferon Res 1993; 13:377-83. [PMID: 8301159 DOI: 10.1089/jir.1993.13.377] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/29/2023]
Abstract
Low levels of the transcription factor ISGF3 alpha were detected in the cytoplasm and nucleus of untreated Daudi cells, which increased markedly following interferon (IFN) treatment. In contrast no ISGF3 alpha was detected in an IFN-resistant clone of Daudi cells, DIF8, and only low levels were detected in these cells after IFN-alpha treatment. High levels of ISGF3 were produced in vitro, however, by the addition of ISGF3 alpha to extracts of IFN-treated DIF8 cells, indicating that IFN is unable to produce substantial amounts of functional ISGF3 alpha in DIF8 cells. A second clone of IFN-resistant Daudi cells, DIF3, also exhibited defective ISGF3 alpha production, which was restored to normal in the subclone DIF3REV5 that had reverted to high IFN sensitivity. Thus, the antiproliferative effect of IFN on Daudi cells and derived clones is closely related to the level of ISGF3 present in the nucleus of these cells. IFN-alpha, however, also enhances the content of ISGF3 gamma in IFN-resistant cells as well as certain proteins of unknown function, raising the possibility that a second pathway of IFN-alpha signal transduction, distinct from the ISGF3 pathway, remains functional in both DIF8 and DIF3 cells.
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Affiliation(s)
- M Dron
- Laboratoire d'oncologie virale, Centre National de la Recherche Scientifique (UPR 274), Villejuif, France
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Dron M, Rebouillat D, Tovey MG. Tandem repeat polymers of a critical region of the human interferon-beta promoter exhibit a marked constitutive activity and enhanced responsiveness to transcriptional regulators in transfected HeLa cells. J Interferon Res 1992; 12:377-87. [PMID: 1431317 DOI: 10.1089/jir.1992.12.377] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/27/2022]
Abstract
Multiple copy tandem repeats polymers of an authentic 30-bp region of the human interferon-beta (IFN-beta) promoter between positions-91 to -62 relative to the cap site or the hexanucleotide GAAAGT derived from this region, both acted as strong constitutive regulatory elements in transfected HeLa cells. Such polymers were unresponsive to treatment with IFN-alpha despite their considerable homology with the IFN-responsive elements of other genes but were highly responsive to treatment of HeLa cells with IFN-gamma. Virus induction of HeLa cells transfected with polymers of the 30-bp region linked to a CAT gene increased the activity of the reporter gene 500- to 2,000-fold over baseline levels. Treatment with IFN-alpha prior to virus induction did not increase further CAT activity. Cotransfection of HeLa cells with the CAT gene under the control of a 12-element tandem repeat polymer of the human IFN-beta promoter and an expression vector for the IRF-1 transcriptional activator markedly increased CAT activity while cotransfection of HeLa cells with the IFN-beta construct together with an expression vector for the transcriptional regulator IRF-2 markedly decreased CAT activity relative to cells transfected with the IFN-beta polymer alone.
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Affiliation(s)
- M Dron
- Laboratory of Viral Oncology, Centre National de la Recherche Scientifique, Villejuif, France
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Abstract
Treatment of Daudi or HeLa cells with human interferon (IFN) alpha 8 before induction with either poly(I)-poly(C) or Sendai virus resulted in an 8- to 100-fold increase in IFN production. The extent of priming in Daudi cells paralleled the increase in the intracellular content of IFN-beta mRNA. IFN-alpha mRNA remained undetectable in poly(I)-poly(C)-treated Daudi cells either before or after priming. An IFN-resistant clone of Daudi cells was found to produce 4- to 20-fold more IFN after priming, indicating that priming was unrelated to the phenotype of IFN sensitivity. IFN treatment of either Daudi or HeLa cells transfected with the human IFN-beta promoter (-282 to -37) linked to the chloramphenicol acetyltransferase (CAT) gene resulted in an increase in CAT activity after induction with poly(I)-poly(C) or Sendai virus. A synthetic double-stranded oligonucleotide corresponding to an authentic 30-base-pair (bp) region of the human IFN-beta promoter between positions -91 and -62 was found to confer virus inducibility upon the reporter CAT gene in HeLa cells. IFN treatment of HeLa cells transfected with this 30-bp region of the IFN-beta promoter in either the correct or reversed orientation also increased CAT activity upon subsequent induction. IFN treatment alone had no detectable effect on the activity of either the 30-bp region or the complete human IFN promoter.
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Affiliation(s)
- M Dron
- Laboratory of Viral Oncology (UPR 274), Centre National de la Recherche Scientifique, Villejuif, France
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