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59. At the Gate of Mutualism: Identification of Genomic Traits Predisposing to Insect-Bacterial Symbiosis in Pathogenic Strains of the Aphid Symbiont Serratia symbiotica

Author

Renoz, François, primary, Foray, Vincent, additional, Ambroise, Jérôme, additional, Baa-Puyoulet, Patrice, additional, Bearzatto, Bertrand, additional, Mendez, Gipsi Lima, additional, Grigorescu, Alina S., additional, Mahillon, Jacques, additional, Mardulyn, Patrick, additional, Gala, Jean-Luc, additional, Calevro, Federica, additional, and Hance, Thierry, additional

Published
2021
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61. GReNaDIne: Data-Driven Approaches to Infer Gene Regulatory Networks in Python

Author

Peignier, Sergio, Schmitt, Pauline, Calevro, Federica, Biologie Fonctionnelle, Insectes et Interactions (BF2I), Institut National des Sciences Appliquées de Lyon (INSA Lyon), and Université de Lyon-Institut National des Sciences Appliquées (INSA)-Université de Lyon-Institut National des Sciences Appliquées (INSA)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE)

Subjects
Machine Learning, Gene Regulatory Networks, Python package, GRN Inference, [INFO.INFO-BI]Computer Science [cs]/Bioinformatics [q-bio.QM], [INFO.INFO-AI]Computer Science [cs]/Artificial Intelligence [cs.AI]
Abstract

GReNaDIne (Gene Regulatory Network Data-driven Inference) is a Python package that implements 18 Machine Learning data-driven gene regulatory network inference methods. It includes 8 generalist pre-processing techniques, suitable for RNAseq and MicroArray datasets analysis, as well as 4 RNAseq normalization techniques. This package has been successfully assessed under the DREAM5 challenge benchmark dataset. The open source GReNaDIne Python package is freely available at https://gitlab.com/bf2i/grenadine as well as its latest documentation https://grenadine.readthedocs.io/en/latest/

Published
2020

62. At the Gate of Mutualism: Identification of Genomic Traits Predisposing to Insect-Bacterial Symbiosis in Pathogenic Strains of the Aphid Symbiont Serratia symbiotica

Author

UCL - SST/LIBST - Louvain Institute of Biomolecular Science and Technology, Renoz, François, Foray, Vincent, Ambroise, Jérôme, Baa-Puyoulet, Patrice, Bearzatto, Bertrand, Lima Mendez, Gipsi, Grigorescu, Alina S., Mahillon, Jacques, Mardulyn, Patrick, Gala, Jean-Luc, Calevro, Federica, Hance, Thierry, UCL - SST/LIBST - Louvain Institute of Biomolecular Science and Technology, Renoz, François, Foray, Vincent, Ambroise, Jérôme, Baa-Puyoulet, Patrice, Bearzatto, Bertrand, Lima Mendez, Gipsi, Grigorescu, Alina S., Mahillon, Jacques, Mardulyn, Patrick, Gala, Jean-Luc, Calevro, Federica, and Hance, Thierry

Abstract

Mutualistic associations between insects and heritable bacterial symbionts are ubiquitous in nature. The aphid symbiont Serratia symbiotica is a valuable candidate for studying the evolution of bacterial symbiosis in insects because it includes a wide diversity of strains that reflect the diverse relationships in which bacteria can be engaged with insects, from pathogenic interactions to obligate intracellular mutualism. The recent discovery of culturable strains, which are hypothesized to resemble the ancestors of intracellular strains, provide an opportunity to study the mechanisms underlying bacterial symbiosis in its early stages. In this study, we analyzed the genomes of three of these culturable strains that are pathogenic to aphid hosts, and performed comparative genomic analyses including mutualistic host-dependent strains. All three genomes are larger than those of the host-restricted S. symbiotica strains described so far, and show significant enrichment in pseudogenes and mobile elements, suggesting that these three pathogenic strains are in the early stages of the adaptation to their host. Compared to their intracellular mutualistic relatives, the three strains harbor a greater diversity of genes coding for virulence factors and metabolic pathways, suggesting that they are likely adapted to infect new hosts and are a potential source of metabolic innovation for insects. The presence in their genomes of secondary metabolism gene clusters associated with the production of antimicrobial compounds and phytotoxins supports the hypothesis that S. symbiotia symbionts evolved from plant-associated strains and that plants may serve as intermediate hosts. Mutualistic associations between insects and bacteria are the result of independent transitions to endosymbiosis initiated by the acquisition of environmental progenitors. In this context, the genomes of free-living S. symbiotica strains provide a rare opportunity to study the inventory of genes held by bacterial

Published
2021

63. At the Gate of Mutualism: Identification of Genomic Traits Predisposing to Insect-Bacterial Symbiosis in Pathogenic Strains of the Aphid Symbiont Serratia symbiotica

Author

Renoz, Francois, Foray, Vincent, Ambroise, Jerome, Baa-Puyoulet, Patrice, Bearzatto, Bertrand, Mendez, Gipsi Lima, Grigorescu, Alina, Mahillon, Jacques, Mardulyn, Patrick, Gala, Jean Luc, Calevro, Federica, Hance, Thierry, Renoz, Francois, Foray, Vincent, Ambroise, Jerome, Baa-Puyoulet, Patrice, Bearzatto, Bertrand, Mendez, Gipsi Lima, Grigorescu, Alina, Mahillon, Jacques, Mardulyn, Patrick, Gala, Jean Luc, Calevro, Federica, and Hance, Thierry

Abstract

Mutualistic associations between insects and heritable bacterial symbionts are ubiquitous in nature. The aphid symbiont Serratia symbiotica is a valuable candidate for studying the evolution of bacterial symbiosis in insects because it includes a wide diversity of strains that reflect the diverse relationships in which bacteria can be engaged with insects, from pathogenic interactions to obligate intracellular mutualism. The recent discovery of culturable strains, which are hypothesized to resemble the ancestors of intracellular strains, provide an opportunity to study the mechanisms underlying bacterial symbiosis in its early stages. In this study, we analyzed the genomes of three of these culturable strains that are pathogenic to aphid hosts, and performed comparative genomic analyses including mutualistic host-dependent strains. All three genomes are larger than those of the host-restricted S. symbiotica strains described so far, and show significant enrichment in pseudogenes and mobile elements, suggesting that these three pathogenic strains are in the early stages of the adaptation to their host. Compared to their intracellular mutualistic relatives, the three strains harbor a greater diversity of genes coding for virulence factors and metabolic pathways, suggesting that they are likely adapted to infect new hosts and are a potential source of metabolic innovation for insects. The presence in their genomes of secondary metabolism gene clusters associated with the production of antimicrobial compounds and phytotoxins supports the hypothesis that S. symbiotia symbionts evolved from plant-associated strains and that plants may serve as intermediate hosts. Mutualistic associations between insects and bacteria are the result of independent transitions to endosymbiosis initiated by the acquisition of environmental progenitors. In this context, the genomes of free-living S. symbiotica strains provide a rare opportunity to study the inventory of genes held by bacterial, SCOPUS: ar.j, info:eu-repo/semantics/published

Published
2021

64. The genome of the cereal pest Sitophilus oryzae: a transposable element haven

Author

Parisot, Nicolas, primary, Vargas-Chavez, Carlos, additional, Goubert, Clément, additional, Baa-Puyoulet, Patrice, additional, Balmand, Séverine, additional, Beranger, Louis, additional, Blanc, Caroline, additional, Bonnamour, Aymeric, additional, Boulesteix, Matthieu, additional, Burlet, Nelly, additional, Calevro, Federica, additional, Callaerts, Patrick, additional, Chancy, Théo, additional, Charles, Hubert, additional, Colella, Stefano, additional, Da Silva Barbosa, André, additional, Dell’Aglio, Elisa, additional, Di Genova, Alex, additional, Febvay, Gérard, additional, Gabaldon, Toni, additional, Galvão Ferrarini, Mariana, additional, Gerber, Alexandra, additional, Gillet, Benjamin, additional, Hubley, Robert, additional, Hughes, Sandrine, additional, Jacquin-Joly, Emmanuelle, additional, Maire, Justin, additional, Marcet-Houben, Marina, additional, Masson, Florent, additional, Meslin, Camille, additional, Montagne, Nicolas, additional, Moya, Andrés, additional, Ribeiro de Vasconcelos, Ana Tereza, additional, Richard, Gautier, additional, Rosen, Jeb, additional, Sagot, Marie-France, additional, Smit, Arian F.A., additional, Storer, Jessica M., additional, Vincent-Monegat, Carole, additional, Vallier, Agnès, additional, Vigneron, Aurélien, additional, Zaidman-Remy, Anna, additional, Zamoum, Waël, additional, Vieira, Cristina, additional, Rebollo, Rita, additional, Latorre, Amparo, additional, and Heddi, Abdelaziz, additional

Published
2021
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66. Evolutionary novelty in the apoptotic pathway of aphids

Author

Ribeiro Lopes, Mélanie, primary, Parisot, Nicolas, additional, Gaget, Karen, additional, Huygens, Cissy, additional, Peignier, Sergio, additional, Duport, Gabrielle, additional, Orlans, Julien, additional, Charles, Hubert, additional, Baatsen, Pieter, additional, Jousselin, Emmanuelle, additional, Da Silva, Pedro, additional, Hens, Korneel, additional, Callaerts, Patrick, additional, and Calevro, Federica, additional

Published
2020
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67. Drosophila-associated bacteria differentially shape the nutritional requirements of their host during juvenile growth

Author

Consuegra, Jessika, primary, Grenier, Théodore, additional, Baa-Puyoulet, Patrice, additional, Rahioui, Isabelle, additional, Akherraz, Houssam, additional, Gervais, Hugo, additional, Parisot, Nicolas, additional, da Silva, Pedro, additional, Charles, Hubert, additional, Calevro, Federica, additional, and Leulier, François, additional

Published
2020
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70. The genome sequence of the grape phylloxera provides insights into the evolution, adaptation, and invasion routes of an iconic pest

Author

European Commission, Ministerio de Economía y Competitividad (España), National Institute of Food and Agriculture (US), Miami University, Rispe, Claude, Legeai, Fabrice, Nabity, Paul D., Fernández, Rosa, Arora, Arinder K., Baa-Puyoulet, Patrice, Banfill, Celeste R., Bao, Leticia, Barberà, Miquel, Bouallègue, Maryem, Bretaudeau, Anthony, Brisson, Jennifer A., Calevro, Federica, Capy, Pierre, Catrice, Olivier, Chertemps, Thomas, Couture, Carole, Delière, Laurent, Douglas, Angela E., Dufault-Thompson, Keith, Escuer, Paula, Feng, Honglin, Forneck, Astrid, Gabaldón, Toni, Guigó, Roderic, Hilliou, Fréderique, Hinojosa-Alvarez, Silvia, Hsiao, Yi-min, Hudaverdian, Sylvie, Jacquin-Joly, Emmanuelle, James, Edward B., Johnston, Spencer, Joubard, Benjamin, Le Goff, Gaëlle, Le Trionnaire, Gaël, Librado, Pablo, Liu, Shanlin, Lombaert, Eric, Lu, Hsiao-ling, Maïbèche-Coisne, Martine, Makni, Mohamed, Marcet-Houben, Marina, Martínez-Torres, David, Meslin, Camille, Montagné, Nicolas, Moran, Nancy A., Papura, Daciana, Parisot, Nicolas, Rahbé, Yvan, Ribeiro Lopes, Mélanie, Ripoll-Cladellas, Aida, Robin, Stéphanie, Roques, Céline, Roux, Pascale, Rozas, Julio, Sánchez-Gracia, Alejandro, Sánchez-Herrero, José F., Santesmasses, Didac, Scatoni, Iris, Serre, Rémy-Félix, Tang, Ming, Tian, Wenhua, Umina, Paul A., Munster, Manuella van, Vincent-Monégat, Carole, Wemmer, Joshua, Wilson, Alex C. C., Zhang, Ying, Zhao, Chaoyang, Zhao, Jing, Zhao, Serena, Zhou, Xin, Delmotte, François, Tagu, Denis, European Commission, Ministerio de Economía y Competitividad (España), National Institute of Food and Agriculture (US), Miami University, Rispe, Claude, Legeai, Fabrice, Nabity, Paul D., Fernández, Rosa, Arora, Arinder K., Baa-Puyoulet, Patrice, Banfill, Celeste R., Bao, Leticia, Barberà, Miquel, Bouallègue, Maryem, Bretaudeau, Anthony, Brisson, Jennifer A., Calevro, Federica, Capy, Pierre, Catrice, Olivier, Chertemps, Thomas, Couture, Carole, Delière, Laurent, Douglas, Angela E., Dufault-Thompson, Keith, Escuer, Paula, Feng, Honglin, Forneck, Astrid, Gabaldón, Toni, Guigó, Roderic, Hilliou, Fréderique, Hinojosa-Alvarez, Silvia, Hsiao, Yi-min, Hudaverdian, Sylvie, Jacquin-Joly, Emmanuelle, James, Edward B., Johnston, Spencer, Joubard, Benjamin, Le Goff, Gaëlle, Le Trionnaire, Gaël, Librado, Pablo, Liu, Shanlin, Lombaert, Eric, Lu, Hsiao-ling, Maïbèche-Coisne, Martine, Makni, Mohamed, Marcet-Houben, Marina, Martínez-Torres, David, Meslin, Camille, Montagné, Nicolas, Moran, Nancy A., Papura, Daciana, Parisot, Nicolas, Rahbé, Yvan, Ribeiro Lopes, Mélanie, Ripoll-Cladellas, Aida, Robin, Stéphanie, Roques, Céline, Roux, Pascale, Rozas, Julio, Sánchez-Gracia, Alejandro, Sánchez-Herrero, José F., Santesmasses, Didac, Scatoni, Iris, Serre, Rémy-Félix, Tang, Ming, Tian, Wenhua, Umina, Paul A., Munster, Manuella van, Vincent-Monégat, Carole, Wemmer, Joshua, Wilson, Alex C. C., Zhang, Ying, Zhao, Chaoyang, Zhao, Jing, Zhao, Serena, Zhou, Xin, Delmotte, François, and Tagu, Denis

Abstract

Background: Although native to North America, the invasion of the aphid-like grape phylloxera Daktulosphaira vitifoliae across the globe altered the course of grape cultivation. For the past 150 years, viticulture relied on grafting-resistant North American Vitis species as rootstocks, thereby limiting genetic stocks tolerant to other stressors such as pathogens and climate change. Limited understanding of the insect genetics resulted in successive outbreaks across the globe when rootstocks failed. Here we report the 294-Mb genome of D. vitifoliae as a basic tool to understand host plant manipulation, nutritional endosymbiosis, and enhance global viticulture. Results: Using a combination of genome, RNA, and population resequencing, we found grape phylloxera showed high duplication rates since its common ancestor with aphids, but similarity in most metabolic genes, despite lacking obligate nutritional symbioses and feeding from parenchyma. Similarly, no enrichment occurred in development genes in relation to viviparity. However, phylloxera evolved > 2700 unique genes that resemble putative effectors and are active during feeding. Population sequencing revealed the global invasion began from the upper Mississippi River in North America, spread to Europe and from there to the rest of the world. Conclusions: The grape phylloxera genome reveals genetic architecture relative to the evolution of nutritional endosymbiosis, viviparity, and herbivory. The extraordinary expansion in effector genes also suggests novel adaptations to plant feeding and how insects induce complex plant phenotypes, for instance galls. Finally, our understanding of the origin of this invasive species and its genome provide genetics resources to alleviate rootstock bottlenecks restricting the advancement of viticulture.

Published
2020

71. Sawfly Genomes Reveal Evolutionary Acquisitions That Fostered the Mega-Radiation of Parasitoid and Eusocial Hymenoptera

Author

Lavrov, Dennis, Lavrov, D ( Dennis ), Oeyen, Jan Philip; https://orcid.org/0000-0002-0116-2234, Baa-Puyoulet, Patrice, Benoit, Joshua B, Beukeboom, Leo W, Bornberg-Bauer, Erich, Buttstedt, Anja, Calevro, Federica, Cash, Elizabeth I, Chao, Hsu, Charles, Hubert, et al, Sotiropoulos, Alexandros G; https://orcid.org/0000-0002-3591-0851, Niehuis, Oliver, Lavrov, Dennis, Lavrov, D ( Dennis ), Oeyen, Jan Philip; https://orcid.org/0000-0002-0116-2234, Baa-Puyoulet, Patrice, Benoit, Joshua B, Beukeboom, Leo W, Bornberg-Bauer, Erich, Buttstedt, Anja, Calevro, Federica, Cash, Elizabeth I, Chao, Hsu, Charles, Hubert, et al, Sotiropoulos, Alexandros G; https://orcid.org/0000-0002-3591-0851, and Niehuis, Oliver

Abstract

The tremendous diversity of Hymenoptera is commonly attributed to the evolution of parasitoidism in the last common ancestor of parasitoid sawflies (Orussidae) and wasp-waisted Hymenoptera (Apocrita). However, Apocrita and Orussidae differ dramatically in their species richness, indicating that the diversification of Apocrita was promoted by additional traits. These traits have remained elusive due to a paucity of sawfly genome sequences, in particular those of parasitoid sawflies. Here, we present comparative analyses of draft genomes of the primarily phytophagous sawfly Athalia rosae and the parasitoid sawfly Orussus abietinus. Our analyses revealed that the ancestral hymenopteran genome exhibited traits that were previously considered unique to eusocial Apocrita (e.g., low transposable element content and activity) and a wider gene repertoire than previously thought (e.g., genes for CO2 detection). Moreover, we discovered that Apocrita evolved a significantly larger array of odorant receptors than sawflies, which could be relevant to the remarkable diversification of Apocrita by enabling efficient detection and reliable identification of hosts.

Published
2020

75. A novel cell death process eliminates both bacteriocytes and their symbionts in the pea aphid/Buchnera symbiotic system

Author

Ribeiro Lopes, Mélanie, Simonet, Pierre, Gaget, Karen, Balmand, Severine, Parisot, Nicolas, Buhler, Kurt, Duport, Marie-Gabrielle, Vulsteke, Veerle, Febvay, Gérard, Heddi, Abdelaziz, Charles, Hubert, Callaerts, Patrick, Calevro, Federica, Charles, Hubert, Biologie Fonctionnelle, Insectes et Interactions (BF2I), Institut National de la Recherche Agronomique (INRA)-Institut National des Sciences Appliquées de Lyon (INSA Lyon), Université de Lyon-Institut National des Sciences Appliquées (INSA)-Université de Lyon-Institut National des Sciences Appliquées (INSA), Université de Lyon, Catholic University of Leuven - Katholieke Universiteit Leuven (KU Leuven), Unité de recherche Productions végétales (CRAG ANT PROD V), Institut National de la Recherche Agronomique (INRA), laboratory of Developmental Genetics, VIB-KUL, Institut National des Sciences Appliquées de Lyon (INSA Lyon), Université de Lyon-Institut National des Sciences Appliquées (INSA)-Université de Lyon-Institut National des Sciences Appliquées (INSA)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), and Institut National des Sciences Appliquées (INSA)-Université de Lyon-Institut National des Sciences Appliquées (INSA)-Université de Lyon

Subjects
[SDV.BIBS] Life Sciences [q-bio]/Quantitative Methods [q-bio.QM], [SDV]Life Sciences [q-bio], Acyrthosiphon pisum, apoptosis, bacteriocyte, artificial diet, [SDV.BIBS]Life Sciences [q-bio]/Quantitative Methods [q-bio.QM], symbiosis, [SDV] Life Sciences [q-bio], transcriptomics, nutrition, cell death, Buchnera, ComputingMilieux_MISCELLANEOUS
Abstract

International audience; Symbiosis is a key source of ecological and evolutionary diversification of eukaryotic organisms throughout the animal and plant kingdoms. In insects that are obligatorily dependent on intracellular bacterial symbionts, novel host cells, the bacteriocytes, have evolved for harboring beneficial microbial partners. These cells constitute a fascinating riddle in developmental cell biology, as their embryonic origin and the molecular mechanisms governing their development and organogenesis, as well as their elimination in response to host physiology, remain largely unsolved.Here we report the discovery of a hitherto unknown cell-death process involved in the degeneration of bacteriocytes in the pea aphid Acyrthosiphon pisum/Buchnera aphidicola symbiotic system, which emerged in recent years as a powerful model for studying symbiotic relationships. This new form of cell death is activated progressively throughout aphid adulthood and exhibits morphological features distinct from evolutionary conserved pathways, including apoptosis- or autophagy-dependent cell deaths. By combining electron microscopy, immunohistochemistry, and molecular analyses, we demonstrated that the initial event of bacteriocyte cell death is the cytoplasmic accumulation of non-autophagic vacuoles, followed by a sequence of cellular stress responses including the formation of autophagosomes in intervacuolar spaces, swelling of bacteriocyte mitochondria, activation of reactive oxygen species, and Buchnera aphidicola endosymbiont degradation by the lysosomal system. This multistep cell-death process originates from the endoplasmic reticulum, an organelle exhibiting a unique reticular network organization in these cells, probably imposed by the presence of millions of Buchnera endosymbionts in each bacteriocyte (Simonet et al., 2018, PNAS, doi: 10.1073/pnas.1720237115). Our findings reveal novel mechanisms by which both bacteriocyte cell and symbiotic bacterial numbers are controlled to maintain organismal homeostasis. They also shed light on previously unknown consequences of persistent obligatory symbiotic bacteria on the cellular organization and functioning of bacteriocytes in their eukaryotic hosts.

Published
2019

76. Bacteriocyte cell death in the pea aphid/symbiotic system

Author

Simonet, Pierre, Gaget, Karen, Balmand, Séverine, Ribeiro Lopes, Mélanie, Parisot, Nicolas, Buhler, Kurt, Duport, Gabrielle, Vulsteke, Veerle, Febvay, Gérard, Heddi, Abdelaziz, Charles, Hubert, Callaerts, Patrick, and Calevro, Federica

Abstract

Symbiotic associations play a pivotal role in multicellular life by facilitating acquisition of new traits and expanding the ecological capabilities of organisms. In insects that are obligatorily dependent on intracellular bacterial symbionts, novel host cells (bacteriocytes) or organs (bacteriomes) have evolved for harboring beneficial microbial partners. The processes regulating the cellular life cycle of these endosymbiont-bearing cells, such as the cell-death mechanisms controlling their fate and elimination in response to host physiology, are fundamental questions in the biology of symbiosis. Here we report the discovery of a cell-death process involved in the degeneration of bacteriocytes in the hemipteran insectThis process is activated progressively throughout aphid adulthood and exhibits morphological features distinct from known cell-death pathways. By combining electron microscopy, immunohistochemistry, and molecular analyses, we demonstrated that the initial event of bacteriocyte cell death is the cytoplasmic accumulation of nonautophagic vacuoles, followed by a sequence of cellular stress responses including the formation of autophagosomes in intervacuolar spaces, activation of reactive oxygen species, andendosymbiont degradation by the lysosomal system. We showed that this multistep cell-death process originates from the endoplasmic reticulum, an organelle exhibiting a unique reticular network organization spread throughout the entire cytoplasm and surroundingendosymbionts. Our findings provide insights into the cellular and molecular processes that coordinate eukaryotic host and endosymbiont homeostasis and death in a symbiotic system and shed light on previously unknown aspects of bacteriocyte biological functioning. ispartof: Proceedings of the National Academy of Sciences of the United States of America vol:115 issue:8 pages:E1819-E1828 ispartof: location:United States status: published

Published
2018

79. Identification of Plant Virus Receptor Candidates in the Stylets of Their Aphid Vectors

Author

Webster, Craig, Pichon, Elodie, Van Munster, Manuella, Monsion, Baptiste, Deshoux, Maelle, Gargani, Daniel, Calevro, Federica, Jimenez, Jaime, Moreno, Aranzazu, Krenz, Björn, Thompson, Jeremy R., Perry, Keith L., Fereres, Alberto, Blanc, Stéphane, Uzest, Marilyne, and Simon, Anne E.

Subjects
Vegetal Biology, Virologie, Virology, fungi, food and beverages, aphid, cuticular protein, plant virus, receptor, stylets, transmission, virologie végétale, pathologie végétale, Biologie végétale
Abstract

Plant viruses transmitted by insects cause tremendous losses in most important crops around the world. The identification of receptors of plant viruses within their insect vectors is a key challenge to understanding the mechanisms of transmission and offers an avenue for future alternative control strategies to limit viral spread. We here report the identification of two cuticular proteins within aphid mouthparts, and we provide experimental support for the role of one of them in the transmission of a noncirculative virus. These two proteins, named Stylin-01 and Stylin-02, belong to the RR-1 cuticular protein subfamily and are highly conserved among aphid species. Using an immunolabeling approach, they were localized in the maxillary stylets of the pea aphid Acyrthosiphon pisum and the green peach aphid Myzus persicae, in the acrostyle, an organ earlier shown to harbor receptors of a noncirculative virus. A peptide motif present at the C termini of both Stylin-01 and Stylin-02 is readily accessible all over the surface of the acrostyle. Competition for in vitro binding to the acrostyle was observed between an antibody targeting this peptide and the helper component protein P2 of Cauliflower mosaic virus. Furthermore, silencing the stylin-01 but not stylin-02 gene through RNA interference decreased the efficiency of Cauliflower mosaic virus transmission by Myzus persicae. These results identify the first cuticular proteins ever reported within arthropod mouthparts and distinguish Stylin-01 as the best candidate receptor for the aphid transmission of noncirculative plant viruses. IMPORTANCE Most noncirculative plant viruses transmitted by insect vectors bind to their mouthparts. They are acquired and inoculated within seconds when insects hop from plant to plant. The receptors involved remain totally elusive due to a long-standing technical bottleneck in working with insect cuticle. Here we characterize the role of the two first cuticular proteins ever identified in arthropod mouthparts. A domain of these proteins is directly accessible at the surface of the cuticle of the acrostyle, an organ at the tip of aphid stylets. The acrostyle has been shown to bind a plant virus, and we consistently demonstrated that one of the identified proteins is involved in viral transmission. Our findings provide an approach to identify proteins in insect mouthparts and point at an unprecedented gene candidate for a plant virus receptor.

Published
2018

80. Evaluating the essentiality of the primary endosymbiont of the rice weevil Sitophilus oryzae through genome analysis

Author

Vargas-Chavez, Carlos, Parisot, Nicolas, Goubert, C., Baa-Puyoulet, Patrice, Balmand, Severine, Boulesteix, M., Burlet, Nelly, Callaerts, Patrick, Charles, Hubert, Colella, Stefano, Febvay, Gérard, Gabaldon, Toni, Jacquin-Joly, Emmanuelle, Loska, Damian, Maire, Justin, MASSON, Florent, Meslin, Camille, montagné, N, Moya, Andres, Vincent-Monégat, Carole, Rebollo, Rita, Vallier, Agnès, Vigneron, Aurélien, Zaidman-Rémy, A., Calevro, Federica, Vieira, Cristina, Latorre, Amparo, Heddi, Abdelaziz, Charles, Hubert, Biologie Fonctionnelle, Insectes et Interactions (BF2I), Institut National de la Recherche Agronomique (INRA)-Institut National des Sciences Appliquées de Lyon (INSA Lyon), Université de Lyon-Institut National des Sciences Appliquées (INSA)-Université de Lyon-Institut National des Sciences Appliquées (INSA), Eléments transposables, évolution, populations, Département génétique, interactions et évolution des génomes [LBBE] (GINSENG), Laboratoire de Biométrie et Biologie Evolutive - UMR 5558 (LBBE), Université Claude Bernard Lyon 1 (UCBL), Université de Lyon-Université de Lyon-Institut National de Recherche en Informatique et en Automatique (Inria)-VetAgro Sup - Institut national d'enseignement supérieur et de recherche en alimentation, santé animale, sciences agronomiques et de l'environnement (VAS)-Centre National de la Recherche Scientifique (CNRS)-Université Claude Bernard Lyon 1 (UCBL), Université de Lyon-Université de Lyon-Institut National de Recherche en Informatique et en Automatique (Inria)-VetAgro Sup - Institut national d'enseignement supérieur et de recherche en alimentation, santé animale, sciences agronomiques et de l'environnement (VAS)-Centre National de la Recherche Scientifique (CNRS)-Laboratoire de Biométrie et Biologie Evolutive - UMR 5558 (LBBE), Université de Lyon-Université de Lyon-Institut National de Recherche en Informatique et en Automatique (Inria)-VetAgro Sup - Institut national d'enseignement supérieur et de recherche en alimentation, santé animale, sciences agronomiques et de l'environnement (VAS)-Centre National de la Recherche Scientifique (CNRS), Catholic University of Leuven - Katholieke Universiteit Leuven (KU Leuven), Laboratoire des symbioses tropicales et méditerranéennes (UMR LSTM), Centre de Coopération Internationale en Recherche Agronomique pour le Développement (Cirad)-Université Montpellier 1 (UM1)-Institut de Recherche pour le Développement (IRD)-Institut National de la Recherche Agronomique (INRA)-Université Montpellier 2 - Sciences et Techniques (UM2)-Université de Montpellier (UM)-Institut national d’études supérieures agronomiques de Montpellier (Montpellier SupAgro), Unité de recherche Productions végétales (CRAG ANT PROD V), Institut National de la Recherche Agronomique (INRA), Barcelona Supercomputing Center - Centro Nacional de Supercomputacion (BSC - CNS), Institut d'écologie et des sciences de l'environnement de Paris (iEES), Institut National de la Recherche Agronomique (INRA)-Université Pierre et Marie Curie - Paris 6 (UPMC)-Université Paris-Est Créteil Val-de-Marne - Paris 12 (UPEC UP12)-Centre National de la Recherche Scientifique (CNRS), Barcelona Institute of Science and Technology (BIST), Department ofComputationaland Systems Biology, University of Pittsburgh (PITT), Pennsylvania Commonwealth System of Higher Education (PCSHE)-Pennsylvania Commonwealth System of Higher Education (PCSHE), Institut Cavanilles de Biodiversitat i Biologia Evolutiva (ICBiBE), Universitat de València (UV), Institut national d'enseignement supérieur pour l'agriculture, l'alimentation et l'environnement (Institut Agro)-Institut national d'enseignement supérieur pour l'agriculture, l'alimentation et l'environnement (Institut Agro), Institut d'Ecologie et des Sciences de l'Environnement de Paris, Institut National de la Recherche Agronomique (INRA)-Université Pierre et Marie Curie - Paris 6 (UPMC)-Institut de Recherche pour le Développement (IRD [France-Ouest])-Université Paris-Est Créteil Val-de-Marne - Paris 12 (UPEC UP12)-Centre National de la Recherche Scientifique (CNRS)-Ecole Normale Supérieure Paris-Saclay (ENS Paris Saclay), Institut National des Sciences Appliquées de Lyon (INSA Lyon), Université de Lyon-Institut National des Sciences Appliquées (INSA)-Université de Lyon-Institut National des Sciences Appliquées (INSA)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), Centre de Coopération Internationale en Recherche Agronomique pour le Développement (Cirad)-Institut de Recherche pour le Développement (IRD)-Université de Montpellier (UM)-Institut national d’études supérieures agronomiques de Montpellier (Montpellier SupAgro), and Institut national d'enseignement supérieur pour l'agriculture, l'alimentation et l'environnement (Institut Agro)-Institut national d'enseignement supérieur pour l'agriculture, l'alimentation et l'environnement (Institut Agro)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE)

Subjects
[SDV.BIBS] Life Sciences [q-bio]/Quantitative Methods [q-bio.QM], fungi, bacteria, food and beverages, biochemical phenomena, metabolism, and nutrition, [SDV.BIBS]Life Sciences [q-bio]/Quantitative Methods [q-bio.QM], Sitophilus oryzae L, symbiosis
Abstract

International audience; The rice weevil Sitophilus oryzae is a pest insect responsible for great economic losses to the agriculture, particularly in developing countries where the damage can exceed 40% of the cereal production. This pest harbors an endosymbiont, “Candidatus Sodalis pierantonius” (cited Sodalis hereafter) that improves its fitness and invasive power. It has been demonstrated that Sodalis recently replaced the ancestral endosymbiont “Candidatus Nardonella” (cited Nardonella hereafter), which is still conserved in other members of the Dryophthoridae family. This recent acquisition raises several challenges for the host, given that the genome of Sodalis has not experienced a drastic genome size shrinkage when compared to other old-lasting insect’s endosymbionts. While the genomes of Sodalis and several strains of Nardonella are available, the insect’s genome is still needed to perform a full study of the system. To this end, we have sequenced and assembled the full genome of the weevil S. oryzae using a combination of Next Generation Sequencing data. Additionally, we have compared this genome with other available insect genomes. We found that the genome of S. oryzae encodes immune elements similar to those of other holometabolous insects, including those living without endosymbionts. Remarkably, an impressive amount of repeated elements was identified, similar to what was previously described in the Sodalis endosymbiont, suggesting the occurrence of gene rearrangement processes at this early phase of symbiogenesis. We concluded that while Sodalis is completely dependent on its host, the insect can survive without its endosymbiont.

Published
2018

81. Bacteriocyte Reprogramming to Cope With Nutritional Stress in a Phloem Sap Feeding Hemipteran, the Pea Aphid Acyrthosiphon pisum

Author

Colella, Stefano, primary, Parisot, Nicolas, additional, Simonet, Pierre, additional, Gaget, Karen, additional, Duport, Gabrielle, additional, Baa-Puyoulet, Patrice, additional, Rahbé, Yvan, additional, Charles, Hubert, additional, Febvay, Gérard, additional, Callaerts, Patrick, additional, and Calevro, Federica, additional

Published
2018
Full Text
View/download PDF

82. Identification of Plant Virus Receptor Candidates in the Stylets of Their Aphid Vectors

Author

Webster, Craig G., primary, Pichon, Elodie, additional, van Munster, Manuella, additional, Monsion, Baptiste, additional, Deshoux, Maëlle, additional, Gargani, Daniel, additional, Calevro, Federica, additional, Jimenez, Jaime, additional, Moreno, Aranzazu, additional, Krenz, Björn, additional, Thompson, Jeremy R., additional, Perry, Keith L., additional, Fereres, Alberto, additional, Blanc, Stéphane, additional, and Uzest, Marilyne, additional

Published
2018
Full Text
View/download PDF

83. Impact of host developmental age on the transcriptome of the symbiotic bacterium Buchnera aphidicolain the pea aphid (Acyrthosiphon pisum)

Author

Bermingham, John, Rabatel, Andreane, Calevro, Federica, Vinuelas, Jose, Febvay, Gerard, Charles, Hubert, Douglas, Angela, and Wilkinson, Tom

Subjects
Gene expression -- Analysis, Host-bacteria relationships -- Analysis, Pea aphid -- Physiological aspects, Biological sciences
Abstract

The various effects of the host developmental age on the transcriptome of the symbiotic bacterium, Buchnera aphidicola present in the pea aphid are discussed. The various functional differences observed between the symbiosis taking place in the adult, as well as embryo insect are also explained.

Published
2009

84. Different levels of transcriptional regulation due to trophic constraints in the reduced genome of Buchnera aphidicola APS

Author

Reymond, Nancie, Calevro, Federica, Vinuelas, Jose, Morin, Nicolas, Rahbe, Yvan, Febvay, Gerard, Laugier, Christian, Douglas, Angela, Fayard, Jean-Michel, and Charles, Hubert

Subjects
Aphididae -- Physiological aspects, Aphididae -- Genetic aspects, Aphididae -- Research, DNA microarrays -- Analysis, Endosymbiosis -- Research, Genetic transcription -- Analysis, Biological sciences
Abstract

Experimental designs with the nutritional physiology of the symbiosis between Buchnera and pea aphids are tested by comparing the omission of essential phenylalanine and the nonessential tyrosine with the presence of dietary amino acids in different ratios. A significant transcriptional regulation is observed at different levels of organization in the Buchnera genome between genes within putative transcription units, and within specific metabolic pathways, despite the absence of regulatory elements.

Published
2006

85. Functional and evolutionary genomics in aphids

Author

Tagu, Denis, Calevro, Federica, Colella, Stefano, Gabaldon, Toni, Sugio, Akiko, Institut de Génétique, Environnement et Protection des Plantes (IGEPP), Institut National de la Recherche Agronomique (INRA)-Université de Rennes 1 (UR1), Université de Rennes (UNIV-RENNES)-Université de Rennes (UNIV-RENNES)-AGROCAMPUS OUEST, Institut national d'enseignement supérieur pour l'agriculture, l'alimentation et l'environnement (Institut Agro)-Institut national d'enseignement supérieur pour l'agriculture, l'alimentation et l'environnement (Institut Agro), Biologie Fonctionnelle, Insectes et Interactions (BF2I), Institut National de la Recherche Agronomique (INRA)-Institut National des Sciences Appliquées de Lyon (INSA Lyon), Institut National des Sciences Appliquées (INSA)-Université de Lyon-Institut National des Sciences Appliquées (INSA)-Université de Lyon, Centre for Genomic Regulation [Barcelona] (CRG), Universitat Pompeu Fabra [Barcelona] (UPF)-Centro Nacional de Analisis Genomico [Barcelona] (CNAG), Vilcinskas, A., Université de Lyon-Institut National des Sciences Appliquées (INSA)-Université de Lyon-Institut National des Sciences Appliquées (INSA), Laboratoire des symbioses tropicales et méditerranéennes (UMR LSTM), Centre de Coopération Internationale en Recherche Agronomique pour le Développement (Cirad)-Université Montpellier 1 (UM1)-Institut de Recherche pour le Développement (IRD)-Institut National de la Recherche Agronomique (INRA)-Université Montpellier 2 - Sciences et Techniques (UM2)-Université de Montpellier (UM)-Institut national d’études supérieures agronomiques de Montpellier (Montpellier SupAgro), Center for Genomic Regulation, Andreas Vilcinskas Editor, Universitat Pompeu Fabra [Barcelona]-Centro Nacional de Analisis Genomico [Barcelona] (CNAG), and Institut National de la Recherche Agronomique (INRA)-Université de Rennes (UR)-AGROCAMPUS OUEST

Subjects
[SDV]Life Sciences [q-bio], [SDE.BE]Environmental Sciences/Biodiversity and Ecology, ComputingMilieux_MISCELLANEOUS
Abstract

International audience; no abstract

Published
2016

86. Specific body compartment phenotypes induced by dsRNA treatments in the pea aphid: the cathepsin-L and phenylalanine hydroxylase examples

Author

Simonet, Pierre, Gaget, Karen, Duport, Marie-Gabrielle, Calevro, Federica, Biologie Fonctionnelle, Insectes et Interactions (BF2I), Institut National de la Recherche Agronomique (INRA)-Institut National des Sciences Appliquées de Lyon (INSA Lyon), Université de Lyon-Institut National des Sciences Appliquées (INSA)-Université de Lyon-Institut National des Sciences Appliquées (INSA), Réseau Biologie Adaptative des Pucerons et des Organismes Associés (BAPOA). Le Rheu, FRA., and ProdInra, Migration

Subjects
[SDV] Life Sciences [q-bio], [SDV]Life Sciences [q-bio], ComputingMilieux_MISCELLANEOUS
Abstract

National audience

Published
2014

87. Métabolisme de la tyrosine et développement parthénogénétique chez le puceron du pois : la fonction centrale de la phenylalanine hydroxylase

Author

Simonet, Pierre, Gaget, Karen, Rey, Marjolaine, Duport, Marie-Gabrielle, Charles, Hubert, Febvay, Gérard, Colella, Stefano, Calevro, Federica, Biologie Fonctionnelle, Insectes et Interactions (BF2I), Institut National de la Recherche Agronomique (INRA)-Institut National des Sciences Appliquées de Lyon (INSA Lyon), Institut National des Sciences Appliquées (INSA)-Université de Lyon-Institut National des Sciences Appliquées (INSA)-Université de Lyon, Réseau Biologie Adaptative des Pucerons et des Organismes Associés (BAPOA). Le Rheu, FRA., and ProdInra, Migration

Subjects
[SDV] Life Sciences [q-bio], [SDV]Life Sciences [q-bio], ComputingMilieux_MISCELLANEOUS
Abstract

National audience

Published
2014

88. Implication de la cathepsine-L dans le remodelage cuticulaire durant le processus de mue chez le puceron du pois, Acyrthosiphon pisum

Author

Simonet, Pierre, Sapountzis, Panagiotis, Duport, Marie-Gabrielle, Balmand, Séverine, Gaget, Karen, Rahbé, Yvan, Colella, Stefano, Charles, Hubert, Febvay, Gérard, Calevro, Federica, Biologie Fonctionnelle, Insectes et Interactions (BF2I), Institut National de la Recherche Agronomique (INRA)-Institut National des Sciences Appliquées de Lyon (INSA Lyon), Institut National des Sciences Appliquées (INSA)-Université de Lyon-Institut National des Sciences Appliquées (INSA)-Université de Lyon, University of Copenhagen = Københavns Universitet (KU), and Réseau Biologie Adaptative des Pucerons et des Organismes Associés (BAPOA). Le Rheu, FRA.

Subjects
[SDV]Life Sciences [q-bio], ComputingMilieux_MISCELLANEOUS
Abstract

National audience

Published
2014

89. Annotating arthropods genome to study and compare their metabolism: the ArthropodaCyc collection of Cyc databases powered by CycADS

Author

Baa-Puyoulet, Patrice, Vellozo, Augusto, Huerta-Cepas, Jaime, Febvay, Gérard, Calevro, Federica, Sagot, Marie-France, Charles, Hubert, Gabaldon, Toni, Colella, Stefano, Biologie Fonctionnelle, Insectes et Interactions (BF2I), Institut National de la Recherche Agronomique (INRA)-Institut National des Sciences Appliquées de Lyon (INSA Lyon), Université de Lyon-Institut National des Sciences Appliquées (INSA)-Université de Lyon-Institut National des Sciences Appliquées (INSA), An algorithmic view on genomes, cells, and environments (BAMBOO), Inria Grenoble - Rhône-Alpes, Institut National de Recherche en Informatique et en Automatique (Inria)-Institut National de Recherche en Informatique et en Automatique (Inria)-Laboratoire de Biométrie et Biologie Evolutive - UMR 5558 (LBBE), Université Claude Bernard Lyon 1 (UCBL), Université de Lyon-Université de Lyon-Institut National de Recherche en Informatique et en Automatique (Inria)-VetAgro Sup - Institut national d'enseignement supérieur et de recherche en alimentation, santé animale, sciences agronomiques et de l'environnement (VAS)-Centre National de la Recherche Scientifique (CNRS)-Université Claude Bernard Lyon 1 (UCBL), Université de Lyon-Université de Lyon-VetAgro Sup - Institut national d'enseignement supérieur et de recherche en alimentation, santé animale, sciences agronomiques et de l'environnement (VAS)-Centre National de la Recherche Scientifique (CNRS), Centro de Regulación Genómica (CRG), Universitat Pompeu Fabra [Barcelona] (UPF), Structural and Computational Biology Unit, European Molecular Biology Laboratory [Hamburg] (EMBL), and Institut National des Sciences Appliquées (INSA)-Université de Lyon-Institut National des Sciences Appliquées (INSA)-Université de Lyon

Subjects
genome annotation, metabolic networks, arthropod genomes, CycADS, BioCyc, ArthopodaCyc, base de données, Bioinformatics, génome, annotation génomique, réseau métabolique, Bio-informatique, arthropode, [INFO.INFO-BI]Computer Science [cs]/Bioinformatics [q-bio.QM], ComputingMilieux_MISCELLANEOUS
Abstract

International audience

Published
2014

90. SymbAphidBase: a new database dedicated to aphid symbionts to store novel sequenced genomes and standardize their annotations

Author

Labernardiere, Mathieu, Baa-Puyoulet, Patrice, Gauthier, Jean-Pierre, Febvay, Gérard, Calevro, Federica, Rahbé, Yvan, Charles, Hubert, Simon, Jean-Christophe, Colella, Stefano, Biologie Fonctionnelle, Insectes et Interactions (BF2I), Institut National de la Recherche Agronomique (INRA)-Institut National des Sciences Appliquées de Lyon (INSA Lyon), Université de Lyon-Institut National des Sciences Appliquées (INSA)-Université de Lyon-Institut National des Sciences Appliquées (INSA), Institut de Génétique, Environnement et Protection des Plantes (IGEPP), Institut National de la Recherche Agronomique (INRA)-Université de Rennes 1 (UR1), Université de Rennes (UNIV-RENNES)-Université de Rennes (UNIV-RENNES)-AGROCAMPUS OUEST, Institut national d'enseignement supérieur pour l'agriculture, l'alimentation et l'environnement (Institut Agro)-Institut national d'enseignement supérieur pour l'agriculture, l'alimentation et l'environnement (Institut Agro), An algorithmic view on genomes, cells, and environments (BAMBOO), Inria Grenoble - Rhône-Alpes, Institut National de Recherche en Informatique et en Automatique (Inria)-Institut National de Recherche en Informatique et en Automatique (Inria)-Laboratoire de Biométrie et Biologie Evolutive - UMR 5558 (LBBE), Université Claude Bernard Lyon 1 (UCBL), Université de Lyon-Université de Lyon-Institut National de Recherche en Informatique et en Automatique (Inria)-VetAgro Sup - Institut national d'enseignement supérieur et de recherche en alimentation, santé animale, sciences agronomiques et de l'environnement (VAS)-Centre National de la Recherche Scientifique (CNRS)-Université Claude Bernard Lyon 1 (UCBL), Université de Lyon-Université de Lyon-VetAgro Sup - Institut national d'enseignement supérieur et de recherche en alimentation, santé animale, sciences agronomiques et de l'environnement (VAS)-Centre National de la Recherche Scientifique (CNRS), ANR Project Speciaphid [ANR-11BSV7-005-01], ANR-11-BSV7-0005,SPECIAPHID,Génétique de l'adaptation trophique et mécanismes d'isolement reproducteur chez les pucerons(2011), Institut National de la Recherche Agronomique (INRA)-Université de Rennes (UR)-AGROCAMPUS OUEST, and Institut National des Sciences Appliquées (INSA)-Université de Lyon-Institut National des Sciences Appliquées (INSA)-Université de Lyon

Subjects
base de données, symbiont, genome annotation, Bioinformatics, puceron, aphid symbionts, SymbAphidBase, genome database, Bio-informatique, annotation génomique, [INFO.INFO-BI]Computer Science [cs]/Bioinformatics [q-bio.QM], ComputingMilieux_MISCELLANEOUS
Abstract

International audience

Published
2014

91. Cathepsin-L proteinase is involved in cuticle remodeling during the molting process in the pea aphid, Acyrthosiphon pisum

Author

Simonet, Pierre, Sapountzis, Panagiotis, Duport, Marie-Gabrielle, Balmand, Séverine, Gaget, Karen, Rahbé, Yvan, Colella, Stefano, Charles, Hubert, Febvay, Gérard, Calevro, Federica, Biologie Fonctionnelle, Insectes et Interactions (BF2I), Institut National de la Recherche Agronomique (INRA)-Institut National des Sciences Appliquées de Lyon (INSA Lyon), Institut National des Sciences Appliquées (INSA)-Université de Lyon-Institut National des Sciences Appliquées (INSA)-Université de Lyon, University of Copenhagen = Københavns Universitet (KU), and Center for Insect Science. Tucson, USA. University of Arizona.

Subjects
[SDV]Life Sciences [q-bio], ComputingMilieux_MISCELLANEOUS
Abstract

International audience

Published
2014

92. Génomique fonctionnelle des interactions bactérie / hôte eucaryote : intégration systémique de données génomiques et métaboliques

Author

Bellvert, Floriant, Calevro, Federica, Charles, Hubert, Colella, Stefano, Febvay, Gérard, Gaillard, Vincent, Kerzaon, Isabelle, Lavire, Céline, Rey, Marjolaine, Laboratoire d'Ingénierie des Systèmes Biologiques et des Procédés (LISBP), Centre National de la Recherche Scientifique (CNRS)-Institut National des Sciences Appliquées - Toulouse (INSA Toulouse), Institut National des Sciences Appliquées (INSA)-Institut National des Sciences Appliquées (INSA)-Institut National de la Recherche Agronomique (INRA), Biologie Fonctionnelle, Insectes et Interactions (BF2I), Institut National de la Recherche Agronomique (INRA)-Institut National des Sciences Appliquées de Lyon (INSA Lyon), Institut National des Sciences Appliquées (INSA)-Université de Lyon-Institut National des Sciences Appliquées (INSA)-Université de Lyon, Ecologie Mircobienne, Institut National de la Recherche Agronomique (INRA), PRES Université de Lyon. Lyon, FRA., ProdInra, Migration, Institut National de la Recherche Agronomique (INRA)-Institut National des Sciences Appliquées - Toulouse (INSA Toulouse), Institut National des Sciences Appliquées (INSA)-Université Fédérale Toulouse Midi-Pyrénées-Institut National des Sciences Appliquées (INSA)-Université Fédérale Toulouse Midi-Pyrénées-Centre National de la Recherche Scientifique (CNRS), Toulouse Biotechnology Institute (TBI), Institut National des Sciences Appliquées - Toulouse (INSA Toulouse), Institut National des Sciences Appliquées (INSA)-Université Fédérale Toulouse Midi-Pyrénées-Institut National des Sciences Appliquées (INSA)-Université Fédérale Toulouse Midi-Pyrénées-Centre National de la Recherche Scientifique (CNRS)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), MetaToul FluxoMet (TBI-MetaToul), MetaboHUB-MetaToul, Génopole Toulouse Midi-Pyrénées [Auzeville] (GENOTOUL), Université Toulouse III - Paul Sabatier (UT3), Université Fédérale Toulouse Midi-Pyrénées-Université Fédérale Toulouse Midi-Pyrénées-Ecole Nationale Vétérinaire de Toulouse (ENVT), Institut National Polytechnique (Toulouse) (Toulouse INP), Université Fédérale Toulouse Midi-Pyrénées-Université Fédérale Toulouse Midi-Pyrénées-Institut National Polytechnique (Toulouse) (Toulouse INP), Université Fédérale Toulouse Midi-Pyrénées-Institut National de la Santé et de la Recherche Médicale (INSERM)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE)-Université Toulouse III - Paul Sabatier (UT3), Université Fédérale Toulouse Midi-Pyrénées-Institut National de la Santé et de la Recherche Médicale (INSERM)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE)-Génopole Toulouse Midi-Pyrénées [Auzeville] (GENOTOUL), Université Fédérale Toulouse Midi-Pyrénées-Institut National de la Santé et de la Recherche Médicale (INSERM)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE)-Toulouse Biotechnology Institute (TBI), Institut National des Sciences Appliquées (INSA)-Université Fédérale Toulouse Midi-Pyrénées-Institut National des Sciences Appliquées (INSA)-Université Fédérale Toulouse Midi-Pyrénées-Centre National de la Recherche Scientifique (CNRS)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE)-Institut National des Sciences Appliquées - Toulouse (INSA Toulouse), Institut National des Sciences Appliquées (INSA)-Université Fédérale Toulouse Midi-Pyrénées-Institut National des Sciences Appliquées (INSA)-Centre National de la Recherche Scientifique (CNRS)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), and Université de Lyon-Institut National des Sciences Appliquées (INSA)-Université de Lyon-Institut National des Sciences Appliquées (INSA)

Subjects
[SDV] Life Sciences [q-bio], [SPI.GPROC] Engineering Sciences [physics]/Chemical and Process Engineering, [SDV]Life Sciences [q-bio], [SDV.IDA]Life Sciences [q-bio]/Food engineering, [SPI.GPROC]Engineering Sciences [physics]/Chemical and Process Engineering, [SDV.IDA] Life Sciences [q-bio]/Food engineering, ComputingMilieux_MISCELLANEOUS
Abstract

National audience

Published
2014

94. Tyrosine metabolism and parthenogenetic development in a symbiotic insect, the pea aphid: the central function of phenylalanine hydroxylase

Author

Simonet, Pierre, Gaget, Karen, Rey, Marjolaine, Duport, Marie-Gabrielle, Charles, Hubert, Febvay, Gérard, Colella, Stefano, Calevro, Federica, Biologie Fonctionnelle, Insectes et Interactions (BF2I), Institut National de la Recherche Agronomique (INRA)-Institut National des Sciences Appliquées de Lyon (INSA Lyon), Institut National des Sciences Appliquées (INSA)-Université de Lyon-Institut National des Sciences Appliquées (INSA)-Université de Lyon, and Center for Insect Science. Tucson, USA. University of Arizona.

Subjects
hydroxylase, phenylalanine, [SDV]Life Sciences [q-bio], buchnera aphidicola, acyrthosiphon pisum, ComputingMilieux_MISCELLANEOUS
Abstract

International audience

Published
2014

95. « ArthropodaCyc » : une collection de bases de données enrichies à l’aide de CycADS pour étudier et comparer le métabolisme des arthropodes

Author

Baa-Puyoulet, Patrice, Colella, Stefano, Vellozo, Augusto, Huerta-Cepas, Jaime, Febvay, Gérard, Calevro, Federica, Gabaldon, Toni, Sagot, Marie-France, Charles, Hubert, Biologie Fonctionnelle, Insectes et Interactions (BF2I), Institut National de la Recherche Agronomique (INRA)-Institut National des Sciences Appliquées de Lyon (INSA Lyon), Université de Lyon-Institut National des Sciences Appliquées (INSA)-Université de Lyon-Institut National des Sciences Appliquées (INSA), An algorithmic view on genomes, cells, and environments (BAMBOO), Inria Grenoble - Rhône-Alpes, Institut National de Recherche en Informatique et en Automatique (Inria)-Institut National de Recherche en Informatique et en Automatique (Inria)-Laboratoire de Biométrie et Biologie Evolutive - UMR 5558 (LBBE), Université Claude Bernard Lyon 1 (UCBL), Université de Lyon-Université de Lyon-Institut National de Recherche en Informatique et en Automatique (Inria)-VetAgro Sup - Institut national d'enseignement supérieur et de recherche en alimentation, santé animale, sciences agronomiques et de l'environnement (VAS)-Centre National de la Recherche Scientifique (CNRS)-Université Claude Bernard Lyon 1 (UCBL), Université de Lyon-Université de Lyon-VetAgro Sup - Institut national d'enseignement supérieur et de recherche en alimentation, santé animale, sciences agronomiques et de l'environnement (VAS)-Centre National de la Recherche Scientifique (CNRS), Centre for Genomic Regulation [Barcelona] (CRG), Universitat Pompeu Fabra [Barcelona] (UPF)-Centro Nacional de Analisis Genomico [Barcelona] (CNAG), Unité de recherche Productions végétales (CRAG ANT PROD V), Institut National de la Recherche Agronomique (INRA), Barcelona Supercomputing Center - Centro Nacional de Supercomputacion (BSC - CNS), Laboratoire de Biométrie et Biologie Evolutive - UMR 5558 (LBBE), Université de Lyon-Université de Lyon-Institut National de Recherche en Informatique et en Automatique (Inria)-VetAgro Sup - Institut national d'enseignement supérieur et de recherche en alimentation, santé animale, sciences agronomiques et de l'environnement (VAS)-Centre National de la Recherche Scientifique (CNRS)-Inria Grenoble - Rhône-Alpes, and Institut National de Recherche en Informatique et en Automatique (Inria)

Subjects
transcriptomics, Buchnera, system biology, Acyrthosiphon pisum, microarray, [SDV.BIBS]Life Sciences [q-bio]/Quantitative Methods [q-bio.QM]
Abstract

International audience; « ArthropodaCyc » : une collection de bases de données enrichies à l’aide de CycADS pour étudier et comparer le métabolisme des arthropodes.Patrice Baa-Puyoulet1, Augusto F. Vellozo2,3, Jaime Huerta-Cepas4, Gérard Febvay1, Federica Calevro1, Toni Gabaldon4, Marie-France Sagot2,3, Hubert Charles1,3 et Stefano Colella1,*.1 UMR203 BF2I, Biologie Fonctionnelle Insectes et Interactions, INRA, INSA-Lyon, Université de Lyon, Villeurbanne, France; 2 Université Lyon 1, CNRS, UMR5558, Laboratoire de Biométrie et Biologie Evolutive, Villeurbanne, France; 3 BAMBOO, INRIA Rhône-Alpes, France; 4 Center for Genomic Regulation, Barcelona, Spain ; * contact : Stefano.Colella@lyon.inra.frAprès la publication de plusieurs génomes d’arthropodes, de nombreuses autres espèces vont être séquencées dans un futur proche, en particulier à travers l’initiative i5ki. La disponibilité de ces multiples séquences ouvre la voie à des études comparatives entre espèces afin de mieux comprendre les différents aspects de la biologie des arthropodes. Ces études nécessitent l’intégration des données génomiques et fonctionnelles en évolution constante : les séquences génomiques et l’annotation fonctionnelle des protéines devant être collectées de sources et méthodes variées et mises à jour régulièrement.Durant l’annotation du génome du puceron du pois (Acyrthosiphon pisum) nous avons développé CycADSii (Cyc Annotation Database System), un système de gestion d’annotations automatisé permettant l’intégration des informations qui sont utilisées pour la reconstruction des réseaux métaboliques. Les données issues de Genbank et/ou de bases de données génomiques spécifiques, ainsi que les annotations fonctionnelles obtenues par les méthodes KAAS-KEGG, PRIAM, Blast2GO, PhylomeDB et MetaPhOrs, sont collectées dans CycADS. Ces annotations sont ensuite extraites, avec possibilité d’appliquer différents filtres de qualité, pour produire les fichiers d’entrée de PathwayTools, un logiciel qui génère et/ou met à jour des bases de données métaboliques de type BioCyc. Nous avons utilisé CycADS pour créer ArthropodaCyciii, une collection de bases de données métaboliques qui, à ce jour, contient 22 arthropodes: [Arachnida] Ixodes scapularis ; [Coleoptera] Tribolium castaneum ; [Crustacea] Daphnia pulex ; [Diptera] Aedes aegypti, Anopheles gambiae, Culex quinquefasciatus, Drosophila melanogaster, Glossina morsitans ; [Hemiptera] Acyrthosiphon pisum, Rhodnius prolixus ; [Hymenoptera] Apis mellifera, Nasonia vitripennis, Atta cephalotes, Acromyrmex echinatior, Camponotus floridanus, Harpegnathos saltator, Linepithema humile, Pogonomyrmex barbatus, Solenopsis invicta, [Lepidoptera] Danaus plexippus, Heliconius melpomene ; [Phthiraptera] Pediculus humanus. Dans ces bases, nous avons ajouté de nombreux liens externes vers les données génomiques de chaque organisme (AphidBase, BeetleBase, VectorBase, Hymenoptera Genome, FlyBase, wFleaBase, MonarchBase, ButterflyGenome) et d’annotation fonctionnelle (Brenda-Enzyme, Gene Ontology, KEGG Orthology et PhylomeDB). Notre collection de bases métaboliques permet alors de réaliser des analyses comparatives en utilisant les fonctionnalités web interactives d’ArthropodaCyc.Dans le futur, nous prévoyons d’ajouter l’annotation métabolique d’autres génomes en cours de séquençage et d’implémenter des passerelles vers des outils d’analyses de réseaux (tels que MetExplore). Nous sommes aussi ouverts à des collaborations sur des projets de séquençage d’arthropodes en cours, pour participer à la première annotation fonctionnelle des protéines et réaliser la reconstruction de leur métabolisme.i http://arthropodgenomes.org/wiki/i5K ii http://www4.inra.fr/cycads/iii http://arthropodacyc.cycadsys.org/

Published
2013

96. Diminution de fécondité et défauts de développement induits par l’inactivation fonctionnelle par RNAi du gène codant la phénylalanine hydroxylase chez le puceron du pois, Acyrthosiphon

Author

Gaget, Karen, Duport, Marie-Gabrielle, Rey, Marjolaine, Balmand, Severine, Charles, Hubert, Febvay, Gérard, Colella, Stefano, Calevro, Federica, Biologie Fonctionnelle, Insectes et Interactions (BF2I), Institut National de la Recherche Agronomique (INRA)-Institut National des Sciences Appliquées de Lyon (INSA Lyon), Université de Lyon-Institut National des Sciences Appliquées (INSA)-Université de Lyon-Institut National des Sciences Appliquées (INSA), Unité de recherche Productions végétales (CRAG ANT PROD V), Institut National de la Recherche Agronomique (INRA), and Charles, Hubert

Subjects
[SDV] Life Sciences [q-bio], parthénogenèse, Buchnera, développement embryonnaire, RNAi, [SDV]Life Sciences [q-bio], Acyrthosiphon pisum, métabolisme, tyrosine, symbiosis
Abstract

International audience; Le puceron du pois est un ravageur important des cultures en région tempérée. Le grand potentiel invasif de cet insecte est essentiellement dû à son système de reproduction, basé pendant le printemps et l’été sur une parthénogenèse vivipare, et à la symbiose obligatoire avec la bactérie Buchnera aphidicola, qui fournit au puceron certains acides aminés essentiels peu présents dans son alimentation. Une étude transcriptomique, récemment conduite dans notre laboratoire, nous a permis de dégager une voie métabolique clé dans le développement parthénogénétique du puceron du pois: la voie de la tyrosine. Afin de mieux caractériser l’importance de cette voie, nous avons étudié l’effet de l’inactivation fonctionnelle par RNAi du gène codant la phénylalanine hydroxylase, enzyme qui transforme la phénylalanine en tyrosine, sur la reproduction parthénogénétique du puceron du pois. L’injection d’ARN doubles-brins dirigés contre ce gène cible de manière privilégiée les compartiments symbiotiques (embryons vivipares et bactériocytes), où nous avons observé une diminution significative de l’expression du gène 1 et 3 jours après l’injection. Les pucerons traités montrent une fécondité réduite (-37 %) et une augmentation (dix fois supérieure) de la mortalité larvaire et de l’apparition de défauts de développement par rapport aux contrôles. Des analyses HPLC sont en cours pour vérifier si les phénotypes observés sont liés à une diminution de la production de tyrosine dans les pucerons traités.

Published
2013

97. Bacteriocyte cell death in the pea aphid/Buchnera symbiotic system.

Author

Simonet, Pierre, Gaget, Karen, Balmand, Séverine, Lopes, Mélanie Ribeiro, Parisot, Nicolas, Duport, Gabrielle, Febvay, Gérard, Heddi, Abdelaziz, Charles, Hubert, Calevro, Federica, Buhler, Kurt, Vulsteke, Veerle, and Callaerts, Patrick

Subjects
PEA aphid, CELL death, CYTOPLASM, BACTERIA, BACTERIAL physiology
Abstract

Symbiotic associations play a pivotal role in multicellular life by facilitating acquisition of new traits and expanding the ecological capabilities of organisms. In insects that are obligatorily dependent on intracellular bacterial symbionts, novel host cells (bacteriocytes) or organs (bacteriomes) have evolved for harboring beneficial microbial partners. The processes regulating the cellular life cycle of these endosymbiont-bearing cells, such as the cell-death mechanisms controlling their fate and elimination in response to host physiology, are fundamental questions in the biology of symbiosis. Here we report the discovery of a cell-death process involved in the degeneration of bacteriocytes in the hemipteran insect Acyrthosiphon pisum. This process is activated progressively throughout aphid adulthood and exhibits morphological features distinct from known cell-death pathways. By combining electron microscopy, immunohistochemistry, and molecular analyses, we demonstrated that the initial event of bacteriocyte cell death is the cytoplasmic accumulation of nonautophagic vacuoles, followed by a sequence of cellular stress responses including the formation of autophagosomes in intervacuolar spaces, activation of reactive oxygen species, and Buchnera endosymbiont degradation by the lysosomal system. We showed that this multistep cell-death process originates from the endoplasmic reticulum, an organelle exhibiting a unique reticular network organization spread throughout the entire cytoplasm and surrounding Buchnera aphidicola endosymbionts. Our findings provide insights into the cellular and molecular processes that coordinate eukaryotic host and endosymbiont homeostasis and death in a symbiotic system and shed light on previously unknown aspects of bacteriocyte biological functioning. [ABSTRACT FROM AUTHOR]

Published
2018
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98. Phenotypic effects of ACYPI007803 knockdown by RNAi in the pea aphid

Author

Rabatel, Andréane, Gaget, Karen, Duport, Marie-Gabrielle, Charles, Hubert, Febvay, Gérard, Colella, Stefano, Calevro, Federica, Charles, Hubert, Biologie Fonctionnelle, Insectes et Interactions (BF2I), Institut National de la Recherche Agronomique (INRA)-Institut National des Sciences Appliquées de Lyon (INSA Lyon), Université de Lyon-Institut National des Sciences Appliquées (INSA)-Université de Lyon-Institut National des Sciences Appliquées (INSA), Unité de recherche Productions végétales (CRAG ANT PROD V), and Institut National de la Recherche Agronomique (INRA)

Subjects
[SDV] Life Sciences [q-bio], [SDV.BIBS] Life Sciences [q-bio]/Quantitative Methods [q-bio.QM], [SDV]Life Sciences [q-bio], [SDV.BIBS]Life Sciences [q-bio]/Quantitative Methods [q-bio.QM], ComputingMilieux_MISCELLANEOUS
Abstract

International audience

Published
2013

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