16 results on '"Tsarmpopoulos, Iason"'
Search Results
2. Molecular and biological characterization of novel and known Sequiviridae members infecting lettuce
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Svanella-Dumas, Laurence, primary, Tsarmpopoulos, Iason, additional, Marais, Armelle, additional, Faure, Chantal, additional, Theil, Sebastien, additional, Glasa, Miroslav, additional, Predajna, Lukas, additional, Gaudin, Jonathan, additional, Tian, Sixing, additional, Porcher, Laetitia, additional, Gentit, Pascal, additional, Leite De Oliveira, Milena, additional, Krause-Sakate, Renate, additional, and Candresse, Thierry, additional
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- 2023
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3. Evolution of the CRISPR-Cas9 defence system following a bacterial host shift
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Ipoutcha, Thomas, primary, Tsarmpopoulos, Iason, additional, Gourgues, Geraldine, additional, Baby, Vincent, additional, Dubos, Paul, additional, Hill, Geoffrey E., additional, Dowling, Andrea, additional, Arfi, Yonathan, additional, Lartigue, Carole, additional, Thebault, Patricia, additional, Bonneaud, Camille, additional, and Sirand-Pugnet, Pascal, additional
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- 2023
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4. A new potyvirus from hedge mustard (Sisymbrium officinale (L.) Scop.) sheds light on the evolutionary history of turnip mosaic virus
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Tsarmpopoulos, Iason, primary, Marais, Armelle, additional, Faure, Chantal, additional, Theil, Sébastien, additional, and Candresse, Thierry, additional
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- 2022
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5. Molecular and Biological Characterization of Novel and Known Family Secoviridae Members Infecting Lettuce.
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Svanella-Dumas, Laurence, Tsarmpopoulos, Iason, Marais, Armelle, Faure, Chantal, Theil, Sébastien, Glasa, Miroslav, Predajna, Lukas, Gaudin, Jonathan, Sixing Tian, Porcher, Laëtitia, Gentit, Pascal, Leite De Oliveira, Milena, Krause-Sakate, Renate, and Candresse, Thierry
- Subjects
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WHOLE genome sequencing , *MOUNTAIN soils , *MOSAIC viruses , *MIXED infections , *NUCLEOTIDE sequencing , *LETTUCE , *GENOMICS , *PHYTOPLASMAS - Abstract
High-throughput sequencing of two lettuces showing virus-like symptoms in France provided evidence of infection by members of the family Secoviridae. One plant (JG1) had a complex mixed infection that involved, among others, a novel waikavirus (lettuce waikavirus 1) and two isolates of a sequivirus related to lettuce mottle virus (LeMoV). The second lettuce plant (JG2) was singly infected by LeMoV. Complete genomic sequences were obtained for all four isolates and, in addition, near complete genome sequences were obtained for other LeMoV or LeMoV-related isolates (from French cultivated and wild lettuces and from a Brazilian cultivated lettuce) and for two isolates of another family Asteraceae-infecting sequivirus, dandelion yellow mosaic virus (DaYMV). Analysis of these genomic sequences allows the proposal of tentative genome organization for the various viruses and clarification of their phylogenetic relationships. Sequence and host range comparisons point to significant differences between the two sequivirus isolates identified in the JG1 plant and LeMoV isolates from France and Brazil, suggesting they belong to a novel species for which the name lettuce star mosaic virus is proposed. [ABSTRACT FROM AUTHOR]
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- 2023
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6. CRISPR/Cas9 : From natural systems towards tools for genome engineering in Mollicutes
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Ipoutcha, Thomas, Tsarmpopoulos, Iason, Gourgues, Geraldine, Thébault, Patricia, Blanchard, Alain, Lartigue, Carole, Sirand-Pugnet, Pascal, Biologie du fruit et pathologie (BFP), Université Bordeaux Segalen - Bordeaux 2-Institut National de la Recherche Agronomique (INRA)-Université Sciences et Technologies - Bordeaux 1, Laboratoire Bordelais de Recherche en Informatique (LaBRI), Université de Bordeaux (UB)-Centre National de la Recherche Scientifique (CNRS)-École Nationale Supérieure d'Électronique, Informatique et Radiocommunications de Bordeaux (ENSEIRB), and ProdInra, Migration
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[SDV.MHEP] Life Sciences [q-bio]/Human health and pathology ,CRISPR/Cas ,[SDV.BA.MVSA]Life Sciences [q-bio]/Animal biology/Veterinary medicine and animal Health ,[SDV.BA] Life Sciences [q-bio]/Animal biology ,[SDV.BA]Life Sciences [q-bio]/Animal biology ,[SDV.BA.MVSA] Life Sciences [q-bio]/Animal biology/Veterinary medicine and animal Health ,ComputingMilieux_MISCELLANEOUS ,[SDV.MHEP]Life Sciences [q-bio]/Human health and pathology - Abstract
National audience
- Published
- 2019
7. Multiple Origins and Specific Evolution of CRISPR/Cas9 Systems in Minimal Bacteria (Mollicutes)
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Ipoutcha, Thomas, primary, Tsarmpopoulos, Iason, additional, Talenton, Vincent, additional, Gaspin, Christine, additional, Moisan, Annick, additional, Walker, Caray A., additional, Brownlie, Joe, additional, Blanchard, Alain, additional, Thebault, Patricia, additional, and Sirand-Pugnet, Pascal, additional
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- 2019
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8. Identification by Next Generation Sequencing (NGS) of three novel viral agents infecting lettuce and belonging to the Betaflexiviridae and Secoviridae families
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Svanella-Dumas, Laurence, Marais-Colombel, Armelle, Tsarmpopoulos, Iason, Faure, Chantal, Theil, Sébastien, Gaudin, Jonathan, Candresse, Thierry, Biologie du fruit et pathologie (BFP), Université Bordeaux Segalen - Bordeaux 2-Institut National de la Recherche Agronomique (INRA)-Université Sciences et Technologies - Bordeaux 1, Unité Mixte de Recherche en Santé Végétale (INRA/ENITA) (UMRSV), Institut National de la Recherche Agronomique (INRA)-École Nationale d'Ingénieurs des Travaux Agricoles - Bordeaux (ENITAB)-Institut des Sciences de la Vigne et du Vin (ISVV), Centre de Coopération Internationale en Recherche Agronomique pour le Développement (CIRAD). FRA., Université Sciences et Technologies - Bordeaux 1-Institut National de la Recherche Agronomique (INRA)-Université Bordeaux Segalen - Bordeaux 2, Unité Mixte de Recherche en Santé Végétale (INRA/ENITA) (UMR SAVE), and ProdInra, Archive Ouverte
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[SDV.MP.VIR] Life Sciences [q-bio]/Microbiology and Parasitology/Virology ,virus phytopathogène ,Etiology ,Next Generation Sequencing ,Lettuce crop ,Plant Virus ,[SDV.BV.PEP]Life Sciences [q-bio]/Vegetal Biology/Phytopathology and phytopharmacy ,phytopathogenic virus ,betaflexiviridae ,santé des plantes ,séquençage ,[SDV.MP.VIR]Life Sciences [q-bio]/Microbiology and Parasitology/Virology ,identification ,recognition of species ,virologie végétale ,plant health ,pathologie végétale ,[SDV.BV.PEP] Life Sciences [q-bio]/Vegetal Biology/Phytopathology and phytopharmacy ,secoviridae - Abstract
UMR BFP - Equipe Virologie; Identification by Next Generation Sequencing (NGS) of three novel viral agents infecting lettuce and belonging to the Betaflexiviridae and Secoviridae families. 16. Rencontres de Virologie Végétale (RVV 2017)
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- 2017
9. Characterization of a natural mycoplasma CRISPR system: towards a new genome editing tool
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Tsarmpopoulos, Iason, Sall, Mamadou, Thébault, Patricia, Gourgues, Géraldine, Talenton, Vincent, Blanchard, Alain, Arfi, Yonathan, Lartigue, Carole, Sirand-Pugnet, Pascal, ProdInra, Migration, Biologie du fruit et pathologie (BFP), Université Sciences et Technologies - Bordeaux 1-Université Bordeaux Segalen - Bordeaux 2-Institut National de la Recherche Agronomique (INRA), Laboratoire Bordelais de Recherche en Informatique (LaBRI), Université de Bordeaux (UB)-Centre National de la Recherche Scientifique (CNRS)-École Nationale Supérieure d'Électronique, Informatique et Radiocommunications de Bordeaux (ENSEIRB), and Université Bordeaux Segalen - Bordeaux 2-Institut National de la Recherche Agronomique (INRA)-Université Sciences et Technologies - Bordeaux 1
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[SDV.MP]Life Sciences [q-bio]/Microbiology and Parasitology ,CRISPR ,mycoplasma ,genome engineering ,[SDV.MP] Life Sciences [q-bio]/Microbiology and Parasitology ,ComputingMilieux_MISCELLANEOUS - Abstract
National audience
- Published
- 2017
10. Cucumber mosaic virus Isolates from Greek Legumes are Associated with Satellite RNAs that are Necrogenic for Tomato
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Giakountis, Antonis, primary, Tsarmpopoulos, Iason, additional, and Chatzivassiliou, Elisavet K., additional
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- 2018
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11. Investigating mycoplasma small non-coding RNAs using synthetic biology tools
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Tsarmpopoulos, Iason, Jollard, Camille, Gourgues, Géraldine, Blanchard, Alain, Dutour, Isabelle, Bourqui, Romain, Moisan, Annick, Chiapello, Hélène, Thébault, Patricia, Lartigue, Carole, Sirand-Pugnet, Pascal, Biologie du fruit et pathologie (BFP), Université Bordeaux Segalen - Bordeaux 2-Institut National de la Recherche Agronomique (INRA)-Université Sciences et Technologies - Bordeaux 1, Laboratoire Bordelais de Recherche en Informatique (LaBRI), Université de Bordeaux (UB)-Centre National de la Recherche Scientifique (CNRS)-École Nationale Supérieure d'Électronique, Informatique et Radiocommunications de Bordeaux (ENSEIRB), Unité de Mathématiques et Informatique Appliquées de Toulouse (MIAT INRA), Institut National de la Recherche Agronomique (INRA), and Mathématiques et Informatique Appliquées du Génome à l'Environnement [Jouy-En-Josas] (MaIAGE)
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[SDV.BA.MVSA]Life Sciences [q-bio]/Animal biology/Veterinary medicine and animal Health ,genome transplantation ,Saccharomyces cerevisiae ,mycoplasma ,genome engineering ,TREC ,ncRNA ,CRISPR/Cas9 ,ComputingMilieux_MISCELLANEOUS ,seamless gene deletion - Abstract
National audience
- Published
- 2016
12. Using CRISPR/Cas9 tools for the engineering of bacterial genome cloned in yeast
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Tsarmpopoulos, Iason, Gourgues, Géraldine, Blanchard, Alain, Lartigue, Carole, Sirand-Pugnet, Pascal, ProdInra, Migration, Biologie du fruit et pathologie (BFP), and Université Bordeaux Segalen - Bordeaux 2-Institut National de la Recherche Agronomique (INRA)-Université Sciences et Technologies - Bordeaux 1
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[SDV.MP]Life Sciences [q-bio]/Microbiology and Parasitology ,genome transplantation ,Saccharomyces cerevisiae ,genome engineering ,mycoplasma ,CRISPR/Cas9 ,[SDV.MP] Life Sciences [q-bio]/Microbiology and Parasitology ,ComputingMilieux_MISCELLANEOUS ,seamless gene deletion - Abstract
International audience
- Published
- 2015
13. In-Yeast Engineering of a Bacterial Genome Using CRISPR/Cas9
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Tsarmpopoulos, Iason, primary, Gourgues, Géraldine, additional, Blanchard, Alain, additional, Vashee, Sanjay, additional, Jores, Joerg, additional, Lartigue, Carole, additional, and Sirand-Pugnet, Pascal, additional
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- 2015
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14. Engineering the genome of minimal bacteria using CRISPR/Cas9 tools
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Tsarmpopoulos, Iason, Pascal Sirand-Pugnet, Cécile Bébéar [Président], Florence Tardy [Rapporteur], Matthieu Jules [Rapporteur], David Bikard, Fabien Darfeuille, Biologie du fruit et pathologie (BFP), Université Sciences et Technologies - Bordeaux 1-Université Bordeaux Segalen - Bordeaux 2-Institut National de la Recherche Agronomique (INRA), Université de Bordeaux, STAR, ABES, Université Bordeaux Segalen - Bordeaux 2-Institut National de la Recherche Agronomique (INRA)-Université Sciences et Technologies - Bordeaux 1, ProdInra, Migration, Sirand-Pugnet, Pascal, Bikard, David, Darfeuille, Fabien, Bébéar, Cécile, Tardy, Florence, and Jules, Matthieu
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[SDV.MP]Life Sciences [q-bio]/Microbiology and Parasitology ,Mycoplasma ,[SDV.BA.MVSA]Life Sciences [q-bio]/Animal biology/Veterinary medicine and animal Health ,[SDV.BA.MVSA] Life Sciences [q-bio]/Animal biology/Veterinary medicine and animal Health ,Synthetic Biology ,Biologie de synthèse ,[SDV.MP] Life Sciences [q-bio]/Microbiology and Parasitology ,CRISPR/Cas9 - Abstract
Mycoplasmas are small pathogenic bacteria that are characterized by reduced genomes of about 1 Mbp with a low G+C content. The interest of the scientific community towards these species has been recently renewed by successful synthesis of their genome and transplantation experiments. These new genetic tools opened the way to further applications and developments for large-scale genome engineering programmes. CRISPR/Cas systems are natural systems that provide bacteria and archaea with an adaptive defense mechanism against invading nucleic acids. The CRISPR system from Streptococcus pyogenes includes an endonuclease (SpCas9) and two CRISPR RNAs (crRNA et tracrRNA) which role are to drive Cas9 to a target sequence. Target recognition depends on a specific pairing of the crRNA and the presence of a motif named protospacer adjacent motif (PAM). After recognition, Cas9 cleaves the targeted DNA. From the natural S. pyogenes system, a simplified genetic tool including Cas9 and a guide RNA (gRNA) was developed for many organisms . The first goal of my thesis was to combine the synthetic biology methods of genome cloning in yeast and back transplantation into recipient cells with a CRISPR/Cas9 tool for efficient engineering of mycoplasma genomes cloned in yeast. We succeeded in removing genes and genomic regions in three different species, Mycoplasma mycoides subsp. capri (Mmc), M. capricolum subsp. capricolum and M. pneumoniae. Then, in order to develop a system optimized for mycoplasma genome editing, we characterized a natural CRISPR/Cas9 system derived from Mycoplasma gallisepticum (Mg). Using a combination of in silico and in vivo approaches, MgCas9 PAM sequence was characterized as NNNAAAA. We then started to develop a minimal CRISPR/Cas system from M. gallisepticum for direct genome editing in mollicutes. Thus we introduced MgCas9 encoding gene in Mmc and tried to activate it with a newly designed gRNA, a chimeric molecule between the crRNA and the tracrRNA of M. gallisepticum, without success yet., Les mycoplasmes sont des bactéries pathogènes, dotées de petits génomes d’environ 1Mbp, avec une faible teneur en G+C. L'intérêt de la communauté scientifique pour ces bactéries a été récemment renouvelé par des avancées dans les domaines de la synthèse et de la transplantation de génomes. Ces nouvelles approches ont ouvert la voie à l'ingénierie génomique à grande échelle des mycoplasmes. Les systèmes CRISPR/Cas sont des systèmes de défense adaptatifs procaryotes contre les acides nucléiques invasifs. Le système CRISPR de Streptococcus pyogenes est composé d’une endonucléase (SpCas9) et de deux CRISPR ARNs (crRNA et tracrRNA) qui dirigent Cas9 vers sa séquence d’ADN cible. La reconnaissance de l’ADN cible se fait par appariement du crRNA et de la présence en aval d’une séquence nommée protospacer adjacent motif (PAM). Apres cette reconnaissance, Cas9 coupe l’ADN cible. A partir de ce système, un outil génétique simplifié composé de Cas9 et d’un ARN guide (gRNA) a été développé pour de nombreux organismes. Le premier objectif de ma thèse était de combiner les méthodes de biologie synthétique de clonage et de la transplantation de génomes avec les outils CRISPR/Cas9 pour l’ingénierie des génomes de mycoplasmes clonés dans la levure. Nous avons réussi à utiliser cette approche pour enlever des gènes et des régions génomiques dans trois espèces: Mycoplasma mycoides subsp. capri (Mmc), M. capricolum subsp. capricolum et M. pneumoniae. Afin de développer un système plus adapté aux mycoplasmes, nous avons ensuite caractérisé le système CRISPR/Cas9 de Mycoplasma gallisepticum (Mg). En utilisant une combinaison d'approches in silico et in vivo, la séquence PAM de MgCas9 a été caractérisée comme NNNAAAA. Nous avons alors entrepris de développer un système CRISPR/Cas minimal de M. gallisepticum pour une utilisation directe dans les cellules de mollicutes: le gène codant MgCas9 a été introduit dans le génome de Mmc, mais son activation avec un gRNA chimère entre le crRNA et le tracrRNA de M. gallisepticum n’a pas été obtenue pour le moment.
15. Evolution of the CRISPR-Cas9 defence system in Mycoplasma gallisepticum following colonization of a novel bird host.
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Ipoutcha T, Tsarmpopoulos I, Gourgues G, Baby V, Dubos P, Hill GE, Arfi Y, Lartigue C, Thébault P, Bonneaud C, and Sirand-Pugnet P
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- Animals, Bacteriophages genetics, Phylogeny, CRISPR-Cas Systems, Mycoplasma gallisepticum genetics, Mycoplasma gallisepticum pathogenicity, Evolution, Molecular
- Abstract
Clustered regularly interspaced short palindromic repeat (CRISPR)-Cas systems are bacterial defences that target bacteriophages and mobile genetic elements. How these defences evolve in novel host environments remains largely unknown. We studied the evolution of the CRISPR-Cas system in Mycoplasma gallisepticum (also named Mycoplasmoides gallisepticum ), a bacterial pathogen of poultry that jumped into a passerine host ~30 years ago. Over the decade following the host shift, all isolates displaying a functional CRISPR-Cas system were found not only to harbour completely new sets of spacers, but the DNA protospacer adjacent motif recognized by the main effector M. gallisepticum Cas9 (MgCas9) was also different. These changes in CRISPR-Cas diversity and specificity are consistent with a change in the community of phages and mobile elements infecting M. gallisepticum as it colonized the novel host. In the years following the host shift, we also detected a gradual rise in isolates displaying non-functional MgCas9. After 12 years, all circulating isolates harboured inactive forms only. This loss of CRISPR-Cas function comes at a time when the passerine host is known to have evolved widespread resistance, which in turn drove the evolution of increasing M. gallisepticum virulence through antagonistic coevolution. Such striking concordance in the rise of inactivated forms of CRISPR-Cas and the evolution of host resistance suggests that the inactivation of the CRISPR-Cas system was necessary for enabling adaptive bacterial responses to host-driven selection. We highlight the need to consider both host and pathogen selection pressures on bacteria for understanding the evolution of CRISPR-Cas systems and the key factors driving the emergence of a pathogenic bacterium in a novel host.
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- 2024
- Full Text
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16. In-Yeast Engineering of a Bacterial Genome Using CRISPR/Cas9.
- Author
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Tsarmpopoulos I, Gourgues G, Blanchard A, Vashee S, Jores J, Lartigue C, and Sirand-Pugnet P
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- Gene Deletion, Genes, Fungal, Genetic Vectors metabolism, Mycoplasma genetics, Plasmids metabolism, RNA, Fungal genetics, CRISPR-Cas Systems genetics, Genetic Engineering methods, Genome, Bacterial, Saccharomyces cerevisiae genetics
- Abstract
One remarkable achievement in synthetic biology was the reconstruction of mycoplasma genomes and their cloning in yeast where they can be modified using available genetic tools. Recently, CRISPR/Cas9 editing tools were developed for yeast mutagenesis. Here, we report their adaptation for the engineering of bacterial genomes cloned in yeast. A seamless deletion of the mycoplasma glycerol-3-phosphate oxidase-encoding gene (glpO) was achieved without selection in one step, using 90 nt paired oligonucleotides as templates to drive recombination. Screening of the resulting clones revealed that more than 20% contained the desired deletion. After manipulation, the overall integrity of the cloned mycoplasma genome was verified by multiplex PCR and PFGE. Finally, the edited genome was back-transplanted into a mycoplasma recipient cell. In accordance with the deletion of glpO, the mutant mycoplasma was affected in the production of H2O2. This work paves the way to high-throughput manipulation of natural or synthetic genomes in yeast.
- Published
- 2016
- Full Text
- View/download PDF
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