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Herr LA, Fiala GJ, Sagar, Schaffer AM, Hummel JF, Zintchenko M, Raute K, Velasco Cárdenas RMH, Heizmann B, Ebert K, Fehrenbach K, Janowska I, Chan S, Tanriver Y, Minguet S, Schamel WW. Kidins220 and Aiolos promote thymic iNKT cell development by reducing TCR signals. Sci Adv 2024; 10:eadj2802. [PMID: 38489359 PMCID: PMC10942104 DOI: 10.1126/sciadv.adj2802] [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] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/25/2023] [Accepted: 02/09/2024] [Indexed: 03/17/2024]
Abstract
Development of T cells is controlled by the signal strength of the TCR. The scaffold protein kinase D-interacting substrate of 220 kilodalton (Kidins220) binds to the TCR; however, its role in T cell development was unknown. Here, we show that T cell-specific Kidins220 knockout (T-KO) mice have strongly reduced invariant natural killer T (iNKT) cell numbers and modest decreases in conventional T cells. Enhanced apoptosis due to increased TCR signaling in T-KO iNKT thymocytes of developmental stages 2 and 3 shows that Kidins220 down-regulates TCR signaling at these stages. scRNA-seq indicated that the transcription factor Aiolos is down-regulated in Kidins220-deficient iNKT cells. Analysis of an Aiolos KO demonstrated that Aiolos is a downstream effector of Kidins220 during iNKT cell development. In the periphery, T-KO iNKT cells show reduced TCR signaling upon stimulation with α-galactosylceramide, suggesting that Kidins220 promotes TCR signaling in peripheral iNKT cells. Thus, Kidins220 reduces or promotes signaling dependent on the iNKT cell developmental stage.
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Affiliation(s)
- Laurenz A. Herr
- Signaling Research Centers BIOSS and CIBSS; University of Freiburg, Freiburg, Germany
- Department of Immunology, Faculty of Biology, University of Freiburg, Freiburg, Germany
- Centre for Chronic Immunodeficiency (CCI), Medical Center, University of Freiburg, Freiburg, Germany
| | - Gina J. Fiala
- Signaling Research Centers BIOSS and CIBSS; University of Freiburg, Freiburg, Germany
- Department of Immunology, Faculty of Biology, University of Freiburg, Freiburg, Germany
- Centre for Chronic Immunodeficiency (CCI), Medical Center, University of Freiburg, Freiburg, Germany
- Spemann Graduate School of Biology and Medicine (SGBM), University of Freiburg, Freiburg, Germany
| | - Sagar
- Department of Medicine II (Gastroenterology, Hepatology, Endocrinology, and Infectious Diseases), Freiburg University Medical Center, Faculty of Medicine, University of Freiburg, Freiburg, Germany
| | - Anna-Maria Schaffer
- Signaling Research Centers BIOSS and CIBSS; University of Freiburg, Freiburg, Germany
- Department of Immunology, Faculty of Biology, University of Freiburg, Freiburg, Germany
- Centre for Chronic Immunodeficiency (CCI), Medical Center, University of Freiburg, Freiburg, Germany
| | - Jonas F. Hummel
- Institute of Medical Microbiology and Hygiene, Medical Center, University of Freiburg, Germany
| | - Marina Zintchenko
- Signaling Research Centers BIOSS and CIBSS; University of Freiburg, Freiburg, Germany
- Department of Immunology, Faculty of Biology, University of Freiburg, Freiburg, Germany
- Centre for Chronic Immunodeficiency (CCI), Medical Center, University of Freiburg, Freiburg, Germany
| | - Katrin Raute
- Signaling Research Centers BIOSS and CIBSS; University of Freiburg, Freiburg, Germany
- Department of Immunology, Faculty of Biology, University of Freiburg, Freiburg, Germany
- Centre for Chronic Immunodeficiency (CCI), Medical Center, University of Freiburg, Freiburg, Germany
- Spemann Graduate School of Biology and Medicine (SGBM), University of Freiburg, Freiburg, Germany
| | - Rubí M.-H. Velasco Cárdenas
- Signaling Research Centers BIOSS and CIBSS; University of Freiburg, Freiburg, Germany
- Department of Immunology, Faculty of Biology, University of Freiburg, Freiburg, Germany
- Centre for Chronic Immunodeficiency (CCI), Medical Center, University of Freiburg, Freiburg, Germany
| | - Beate Heizmann
- Institut de Génétique et de Biologie Moléculaire et Cellulaire (IGBMC), INSERM U1258, CNRS UMR7104, Université de Strasbourg, Illkirch, France
| | - Karolina Ebert
- Institute of Medical Microbiology and Hygiene, Medical Center, University of Freiburg, Germany
| | - Kerstin Fehrenbach
- Signaling Research Centers BIOSS and CIBSS; University of Freiburg, Freiburg, Germany
- Department of Immunology, Faculty of Biology, University of Freiburg, Freiburg, Germany
- Centre for Chronic Immunodeficiency (CCI), Medical Center, University of Freiburg, Freiburg, Germany
| | - Iga Janowska
- Signaling Research Centers BIOSS and CIBSS; University of Freiburg, Freiburg, Germany
- Department of Immunology, Faculty of Biology, University of Freiburg, Freiburg, Germany
- Centre for Chronic Immunodeficiency (CCI), Medical Center, University of Freiburg, Freiburg, Germany
| | - Susan Chan
- Institut de Génétique et de Biologie Moléculaire et Cellulaire (IGBMC), INSERM U1258, CNRS UMR7104, Université de Strasbourg, Illkirch, France
| | - Yakup Tanriver
- Institute of Medical Microbiology and Hygiene, Medical Center, University of Freiburg, Germany
- Department of Medicine IV: Nephrology and Primary Care, Medical Center, University of Freiburg, Freiburg, Germany
| | - Susana Minguet
- Signaling Research Centers BIOSS and CIBSS; University of Freiburg, Freiburg, Germany
- Department of Immunology, Faculty of Biology, University of Freiburg, Freiburg, Germany
- Centre for Chronic Immunodeficiency (CCI), Medical Center, University of Freiburg, Freiburg, Germany
- Spemann Graduate School of Biology and Medicine (SGBM), University of Freiburg, Freiburg, Germany
| | - Wolfgang W. Schamel
- Signaling Research Centers BIOSS and CIBSS; University of Freiburg, Freiburg, Germany
- Department of Immunology, Faculty of Biology, University of Freiburg, Freiburg, Germany
- Centre for Chronic Immunodeficiency (CCI), Medical Center, University of Freiburg, Freiburg, Germany
- Spemann Graduate School of Biology and Medicine (SGBM), University of Freiburg, Freiburg, Germany
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Demont T, Horta-Sáenz D, Raiber E. Exposure to worrisome topics can increase cognitive performance when incentivized by a performance goal. Sci Rep 2024; 14:1204. [PMID: 38216640 PMCID: PMC10786830 DOI: 10.1038/s41598-023-50036-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2023] [Accepted: 12/14/2023] [Indexed: 01/14/2024] Open
Abstract
Worrisome topics, such as climate change, economic crises, or pandemics including Covid-19, are increasingly present and pervasive due to digital media and social networks. Do worries triggered by such topics affect the cognitive capacities of young adults? In an online experiment during the Covid-19 pandemic (N=1503), we test how the cognitive performance of university students responds when exposed to topics discussing (i) current adverse mental health consequences of social restrictions or (ii) future labor market hardships linked to the economic contraction. Moreover, we study how such a response is affected by a performance goal. We find that the labor market topic increases cognitive performance when it is motivated by a goal, consistent with a 'tunneling effect' of scarcity or a positive stress effect. However, we show that the positive reaction is mainly concentrated among students with larger financial and social resources, pointing to an inequality-widening mechanism. Conversely, we find limited support for a negative stress effect or a 'cognitive load effect' of scarcity, as the mental health topic has a negative but insignificant average effect on cognitive performance. Yet, there is a negative response among psychologically vulnerable individuals when the payout is not conditioned on reaching a goal.
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Affiliation(s)
- Timothée Demont
- Aix Marseille University, CNRS, AMSE, Marseille, 5-9 Boulevard Maurice Bourdet, 13001, Marseille, France
| | - Daniela Horta-Sáenz
- Aix Marseille University, CNRS, AMSE, Marseille, 5-9 Boulevard Maurice Bourdet, 13001, Marseille, France
| | - Eva Raiber
- Aix Marseille University, CNRS, AMSE, Marseille, 5-9 Boulevard Maurice Bourdet, 13001, Marseille, France.
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3
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Jouan R, Lextrait G, Lachat J, Yokota A, Cossard R, Naquin D, Timchenko T, Kikuchi Y, Ohbayashi T, Mergaert P. Transposon sequencing reveals the essential gene set and genes enabling gut symbiosis in the insect symbiont Caballeronia insecticola. ISME Commun 2024; 4:ycad001. [PMID: 38282642 PMCID: PMC10809759 DOI: 10.1093/ismeco/ycad001] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 09/06/2023] [Revised: 10/10/2023] [Accepted: 11/03/2023] [Indexed: 01/30/2024]
Abstract
Caballeronia insecticola is a bacterium belonging to the Burkholderia genus sensu lato, which is able to colonize multiple environments like soils and the gut of the bean bug Riptortus pedestris. We constructed a saturated Himar1 mariner transposon library and revealed by transposon-sequencing that 498 protein-coding genes constitute the essential genome of Caballeronia insecticola for growth in free-living conditions. By comparing essential gene sets of Caballeronia insecticola and seven related Burkholderia s.l. strains, only 120 common genes were identified, indicating that a large part of the essential genome is strain-specific. In order to reproduce specific nutritional conditions that are present in the gut of Riptortus pedestris, we grew the mutant library in minimal media supplemented with candidate gut nutrients and identified several condition-dependent fitness-defect genes by transposon-sequencing. To validate the robustness of the approach, insertion mutants in six fitness genes were constructed and their growth deficiency in media supplemented with the corresponding nutrient was confirmed. The mutants were further tested for their efficiency in Riptortus pedestris gut colonization, confirming that gluconeogenic carbon sources, taurine and inositol, are nutrients consumed by the symbiont in the gut. Thus, our study provides insights about specific contributions provided by the insect host to the bacterial symbiont.
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Grants
- JSPS Research Fellowship for Young Scientists, Japan
- Ministry of Education, Culture, Sports, Science, and Technology (MEXT), Japan
- Ministry of Higher Education, Research, and Innovation, France
- CNRS International Research Project, France
- JSPS-CNRS Bilateral Open Partnership Joint Research Project, France-Japan
- Agence Nationale de la Recherche, France
- Saclay Plant Sciences-SPS
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Affiliation(s)
- Romain Jouan
- Université Paris-Saclay, CEA, CNRS, Institute for Integrative Biology of the Cell (I2BC), Gif-sur-Yvette 91198, France
| | - Gaëlle Lextrait
- Université Paris-Saclay, CEA, CNRS, Institute for Integrative Biology of the Cell (I2BC), Gif-sur-Yvette 91198, France
| | - Joy Lachat
- Université Paris-Saclay, CEA, CNRS, Institute for Integrative Biology of the Cell (I2BC), Gif-sur-Yvette 91198, France
| | - Aya Yokota
- Université Paris-Saclay, CEA, CNRS, Institute for Integrative Biology of the Cell (I2BC), Gif-sur-Yvette 91198, France
| | - Raynald Cossard
- Université Paris-Saclay, CEA, CNRS, Institute for Integrative Biology of the Cell (I2BC), Gif-sur-Yvette 91198, France
| | - Delphine Naquin
- Université Paris-Saclay, CEA, CNRS, Institute for Integrative Biology of the Cell (I2BC), Gif-sur-Yvette 91198, France
| | - Tatiana Timchenko
- Université Paris-Saclay, CEA, CNRS, Institute for Integrative Biology of the Cell (I2BC), Gif-sur-Yvette 91198, France
| | - Yoshitomo Kikuchi
- Bioproduction Research Institute, National Institute of Advanced Industrial Science and Technology (AIST), Hokkaido Center, Sapporo 062-8517, Japan
| | - Tsubasa Ohbayashi
- Université Paris-Saclay, CEA, CNRS, Institute for Integrative Biology of the Cell (I2BC), Gif-sur-Yvette 91198, France
- Institute for Agro-Environmental Sciences, National Agriculture and Food Research Organization (NARO), Tsukuba 305-8604, Japan
| | - Peter Mergaert
- Université Paris-Saclay, CEA, CNRS, Institute for Integrative Biology of the Cell (I2BC), Gif-sur-Yvette 91198, France
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4
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Saclier N, Duchemin L, Konecny-Dupré L, Grison P, Eme D, Martin C, Callou C, Lefébure T, François C, Issartel C, Lewis JJ, Stoch F, Sket B, Gottstein S, Delić T, Zagmajster M, Grabowski M, Weber D, Reboleira ASPS, Palatov D, Paragamian K, Knight LRFD, Michel G, Lefebvre F, Hosseini MJM, Camacho AI, De Bikuña BG, Taleb A, Belaidi N, Tuekam Kayo RP, Galassi DMP, Moldovan OT, Douady CJ, Malard F. A collaborative backbone resource for comparative studies of subterranean evolution: The World Asellidae database. Mol Ecol Resour 2024; 24:e13882. [PMID: 37864541 DOI: 10.1111/1755-0998.13882] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/19/2023] [Revised: 09/09/2023] [Accepted: 10/04/2023] [Indexed: 10/23/2023]
Abstract
Transition to novel environments, such as groundwater colonization by surface organisms, provides an excellent research ground to study phenotypic evolution. However, interspecific comparative studies on evolution to groundwater life are few because of the challenge in assembling large ecological and molecular resources for species-rich taxa comprised of surface and subterranean species. Here, we make available to the scientific community an operational set of working tools and resources for the Asellidae, a family of freshwater isopods containing hundreds of surface and subterranean species. First, we release the World Asellidae database (WAD) and its web application, a sustainable and FAIR solution to producing and sharing data and biological material. WAD provides access to thousands of species occurrences, specimens, DNA extracts and DNA sequences with rich metadata ensuring full scientific traceability. Second, we perform a large-scale dated phylogenetic reconstruction of Asellidae to support phylogenetic comparative analyses. Of 424 terminal branches, we identify 34 pairs of surface and subterranean species representing independent replicates of the transition from surface water to groundwater. Third, we exemplify the usefulness of WAD for documenting phenotypic shifts associated with colonization of subterranean habitats. We provide the first phylogenetically controlled evidence that body size of males decreases relative to that of females upon groundwater colonization, suggesting competition for rare receptive females selects for smaller, more agile males in groundwater. By making these tools and resources widely accessible, we open up new opportunities for exploring how phenotypic traits evolve in response to changes in selective pressures and trade-offs during groundwater colonization.
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Affiliation(s)
- Nathanaelle Saclier
- Univ Lyon, Université Claude Bernard Lyon 1, CNRS, ENTPE, UMR 5023 LEHNA, Villeurbanne, France
- ISEM, CNRS, Univ. Montpellier, IRD, EPHE, Montpellier, France
| | - Louis Duchemin
- Univ Lyon, Université Claude Bernard Lyon 1, CNRS, ENTPE, UMR 5023 LEHNA, Villeurbanne, France
| | - Lara Konecny-Dupré
- Univ Lyon, Université Claude Bernard Lyon 1, CNRS, ENTPE, UMR 5023 LEHNA, Villeurbanne, France
| | - Philippe Grison
- BBEES, Unité Bases de données sur la Biodiversité, Ecologie, Environnement et Sociétés, Muséum National d'Histoire Naturelle, CNRS, Paris, France
| | - David Eme
- INRAE, UR-RiverLY, Centre Lyon-Grenoble Auvergne-Rhône-Alpes, Villeurbanne, France
| | - Chloé Martin
- BBEES, Unité Bases de données sur la Biodiversité, Ecologie, Environnement et Sociétés, Muséum National d'Histoire Naturelle, CNRS, Paris, France
| | - Cécile Callou
- BBEES, Unité Bases de données sur la Biodiversité, Ecologie, Environnement et Sociétés, Muséum National d'Histoire Naturelle, CNRS, Paris, France
| | - Tristan Lefébure
- Univ Lyon, Université Claude Bernard Lyon 1, CNRS, ENTPE, UMR 5023 LEHNA, Villeurbanne, France
| | - Clémentine François
- Univ Lyon, Université Claude Bernard Lyon 1, CNRS, ENTPE, UMR 5023 LEHNA, Villeurbanne, France
| | - Colin Issartel
- Univ Lyon, Université Claude Bernard Lyon 1, CNRS, ENTPE, UMR 5023 LEHNA, Villeurbanne, France
| | - Julian J Lewis
- Virginia Museum of Natural History, Martinsville, Virginia, USA
- Lewis and Associates, Cave, Karst and Groundwater Biological Consulting, Borden, Indiana, USA
| | - Fabio Stoch
- Evolutionary Biology & Ecology, Université libre de Bruxelles (ULB), Bruxelles, Belgium
| | - Boris Sket
- Department of Biology, SubBio Lab, Biotechnical Faculty, University of Ljubljana, Ljubljana, Slovenia
| | - Sanja Gottstein
- Faculty of Science, Department of Biology, University of Zagreb, Zagreb, Croatia
| | - Teo Delić
- Department of Biology, SubBio Lab, Biotechnical Faculty, University of Ljubljana, Ljubljana, Slovenia
| | - Maja Zagmajster
- Department of Biology, SubBio Lab, Biotechnical Faculty, University of Ljubljana, Ljubljana, Slovenia
| | - Michal Grabowski
- Department of Invertebrate Zoology & Hydrobiology, Faculty of Biology & Environmental Protection, University of Lodz, Lodz, Poland
| | - Dieter Weber
- Musée National d'Histoire Naturelle de Luxembourg, Luxembourg City, Luxembourg
- Senckenberg Deutsches Entomologisches Institut, Müncheberg, Germany
| | - Ana Sofia P S Reboleira
- Departamento de Biologia Animal, and Centre for Ecology, Evolution and Environmental Changes & CHANGE - Global Change and Sustainability Institute, Faculdade de Ciências, Universidade de Lisboa, Lisbon, Portugal
- Natural History Museum of Denmark, University of Copenhagen, Copenhagen, Denmark
| | - Dmitry Palatov
- A.N. Severtsov Institute of Ecology and Evolution of the Russian Academy of Sciences, Moscow, Russia
| | | | | | - Georges Michel
- CWEPSS, Commission Wallonne d'Etude et de Protection des Sites Souterrains, Bruxelles, Belgium
| | | | - Mohammad-Javad Malek Hosseini
- Jovan Hadži Institute of Biology, Research Centre of the Slovenian Academy of Sciences and Arts (ZRC-SAZU), Ljubljana, Slovenia
- Department of Organisms and Ecosystems Research, National Institute of Biology (NIB), Ljubljana, Slovenia
| | - Ana I Camacho
- Museo Nacional de Ciencias Naturales (CSIC). Dpto. Biodiversidad y Biología Evolutiva, Madrid, Spain
| | - Begoña Gartzia De Bikuña
- Anbiotek, Investigación científica y técnica del medio ambiente, Erandio, Bizkaia, Spain
- Anbiolab, BIC Bizkaia Astondo bidea, Derio, Spain
| | - Amina Taleb
- Laboratoire d'Écologie et Gestion des Ecosystèmes Naturels, University of Tlemcen, Tlemcen, Algeria
| | - Nouria Belaidi
- Laboratoire d'Écologie et Gestion des Ecosystèmes Naturels, University of Tlemcen, Tlemcen, Algeria
| | - Raoul P Tuekam Kayo
- Faculty of Science, Department of Zoology, University of Bamenda, Bambili, Cameroon
| | | | - Oana Teodora Moldovan
- Emil Racovita Institute of Speleology, Cluj-Napoca, Romania
- Centro Nacional de Investigación sobre la Evolución Humana, Burgos, Spain
| | - Christophe J Douady
- Univ Lyon, Université Claude Bernard Lyon 1, CNRS, ENTPE, UMR 5023 LEHNA, Villeurbanne, France
- Institut Universitaire de France, Paris, France
| | - Florian Malard
- Univ Lyon, Université Claude Bernard Lyon 1, CNRS, ENTPE, UMR 5023 LEHNA, Villeurbanne, France
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Snounou G, Sharp PM, Culleton R. The two parasite species formerly known as Plasmodium ovale. Trends Parasitol 2024; 40:21-27. [PMID: 38040603 DOI: 10.1016/j.pt.2023.11.004] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [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] [Received: 10/20/2023] [Revised: 11/09/2023] [Accepted: 11/09/2023] [Indexed: 12/03/2023]
Abstract
Plasmodium ovale was the last of the exclusively human malaria parasites to be described, in 1922, and has remained the least well studied. Beginning in 1995, two divergent forms of the parasite, later termed 'classic' and 'variant', were described. By 2010, it was realised that these forms are two closely related, but genetically distinct and non-recombining species; they were given the names Plasmodium ovale curtisi and Plasmodium ovale wallikeri. Since then, substantial additional data have confirmed that the two parasites are indeed separate species, but the trinomial nomenclature has often led to confusion about their status, with many authors describing them as subspecies. We hereby formally name them Plasmodium ovalecurtisi and Plasmodium ovalewallikeri.
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Affiliation(s)
- Georges Snounou
- Université Paris-Saclay, Inserm, CEA, Immunologie des maladies virales, auto-immunes, hématologiques et bactériennes (IMVA-HB/IDMIT/UMR1184), 92265, Fontenay-aux-Roses & Kremlin-Bicêtre, France.
| | - Paul M Sharp
- Institute of Ecology and Evolution, University of Edinburgh, Edinburgh EH9 3FL, UK
| | - Richard Culleton
- Department of Molecular Parasitology, Proteo-Science Centre, Ehime University, 454 Shitsukawa, Toon, Ehime 791-0295, Japan.
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6
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Nevers Q, Scrima N, Glon D, Le Bars R, Decombe A, Garnier N, Ouldali M, Lagaudrière-Gesbert C, Blondel D, Albertini A, Gaudin Y. Properties of rabies virus phosphoprotein and nucleoprotein biocondensates formed in vitro and in cellulo. PLoS Pathog 2022; 18:e1011022. [PMID: 36480574 PMCID: PMC9767369 DOI: 10.1371/journal.ppat.1011022] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/03/2022] [Revised: 12/20/2022] [Accepted: 11/23/2022] [Indexed: 12/13/2022] Open
Abstract
Rabies virus (RABV) transcription and replication take place within viral factories having liquid properties, called Negri bodies (NBs), that are formed by liquid-liquid phase separation (LLPS). The co-expression of RABV nucleoprotein (N) and phosphoprotein (P) in mammalian cells is sufficient to induce the formation of cytoplasmic biocondensates having properties that are like those of NBs. This cellular minimal system was previously used to identify P domains that are essential for biocondensates formation. Here, we constructed fluorescent versions of N and analyzed by FRAP their dynamics inside the biocondensates formed in this minimal system as well as in NBs of RABV-infected cells using FRAP. The behavior of N appears to be different of P as there was no fluorescence recovery of N proteins after photobleaching. We also identified arginine residues as well as two exposed loops of N involved in condensates formation. Corresponding N mutants exhibited distinct phenotypes in infected cells ranging from co-localization with NBs to exclusion from them associated with a dominant-negative effect on infection. We also demonstrated that in vitro, in crowded environments, purified P as well as purified N0-P complex (in which N is RNA-free) form liquid condensates. We identified P domains required for LLPS in this acellular system. P condensates were shown to associate with liposomes, concentrate RNA, and undergo a liquid-gel transition upon ageing. Conversely, N0-P droplets were disrupted upon incubation with RNA. Taken together, our data emphasize the central role of P in NBs formation and reveal some physicochemical features of P and N0-P droplets relevant for explaining NBs properties such as their envelopment by cellular membranes at late stages of infection and nucleocapsids ejections from the viral factories.
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Affiliation(s)
- Quentin Nevers
- Institute for Integrative Biology of the Cell (I2BC), CEA, CNRS, Université Paris-Saclay, Gif-sur-Yvette, France
| | - Nathalie Scrima
- Institute for Integrative Biology of the Cell (I2BC), CEA, CNRS, Université Paris-Saclay, Gif-sur-Yvette, France
| | - Damien Glon
- Institute for Integrative Biology of the Cell (I2BC), CEA, CNRS, Université Paris-Saclay, Gif-sur-Yvette, France
| | - Romain Le Bars
- Institute for Integrative Biology of the Cell (I2BC), CEA, CNRS, Université Paris-Saclay, Gif-sur-Yvette, France
| | - Alice Decombe
- Institute for Integrative Biology of the Cell (I2BC), CEA, CNRS, Université Paris-Saclay, Gif-sur-Yvette, France
| | - Nathalie Garnier
- Institute for Integrative Biology of the Cell (I2BC), CEA, CNRS, Université Paris-Saclay, Gif-sur-Yvette, France
| | - Malika Ouldali
- Institute for Integrative Biology of the Cell (I2BC), CEA, CNRS, Université Paris-Saclay, Gif-sur-Yvette, France
| | - Cécile Lagaudrière-Gesbert
- Institute for Integrative Biology of the Cell (I2BC), CEA, CNRS, Université Paris-Saclay, Gif-sur-Yvette, France
| | - Danielle Blondel
- Institute for Integrative Biology of the Cell (I2BC), CEA, CNRS, Université Paris-Saclay, Gif-sur-Yvette, France
| | - Aurélie Albertini
- Institute for Integrative Biology of the Cell (I2BC), CEA, CNRS, Université Paris-Saclay, Gif-sur-Yvette, France
| | - Yves Gaudin
- Institute for Integrative Biology of the Cell (I2BC), CEA, CNRS, Université Paris-Saclay, Gif-sur-Yvette, France
- * E-mail:
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7
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Wang Y, Xue H, Pourcel C, Du Y, Gautheret D. 2-kupl: mapping-free variant detection from DNA-seq data of matched samples. BMC Bioinformatics 2021; 22:304. [PMID: 34090332 PMCID: PMC8180056 DOI: 10.1186/s12859-021-04185-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/03/2021] [Accepted: 05/11/2021] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND The detection of genome variants, including point mutations, indels and structural variants, is a fundamental and challenging computational problem. We address here the problem of variant detection between two deep-sequencing (DNA-seq) samples, such as two human samples from an individual patient, or two samples from distinct bacterial strains. The preferred strategy in such a case is to align each sample to a common reference genome, collect all variants and compare these variants between samples. Such mapping-based protocols have several limitations. DNA sequences with large indels, aggregated mutations and structural variants are hard to map to the reference. Furthermore, DNA sequences cannot be mapped reliably to genomic low complexity regions and repeats. RESULTS We introduce 2-kupl, a k-mer based, mapping-free protocol to detect variants between two DNA-seq samples. On simulated and actual data, 2-kupl achieves higher accuracy than other mapping-free protocols. Applying 2-kupl to prostate cancer whole exome sequencing data, we identify a number of candidate variants in hard-to-map regions and propose potential novel recurrent variants in this disease. CONCLUSIONS We developed a mapping-free protocol for variant calling between matched DNA-seq samples. Our protocol is suitable for variant detection in unmappable genome regions or in the absence of a reference genome.
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Affiliation(s)
- Yunfeng Wang
- Institute of Integrative Cell Biology (I2BC), Université Paris-Saclay, CNRS, CEA, 1 avenue de la Terrasse, 91190 Gif-sur-Yvette, France
- Annoroad Gene Technology Co., Ltd, Beijing, 100176 China
| | - Haoliang Xue
- Institute of Integrative Cell Biology (I2BC), Université Paris-Saclay, CNRS, CEA, 1 avenue de la Terrasse, 91190 Gif-sur-Yvette, France
| | - Christine Pourcel
- Institute of Integrative Cell Biology (I2BC), Université Paris-Saclay, CNRS, CEA, 1 avenue de la Terrasse, 91190 Gif-sur-Yvette, France
| | - Yang Du
- Annoroad Gene Technology Co., Ltd, Beijing, 100176 China
| | - Daniel Gautheret
- Institute of Integrative Cell Biology (I2BC), Université Paris-Saclay, CNRS, CEA, 1 avenue de la Terrasse, 91190 Gif-sur-Yvette, France
- IHU PRISM, Gustave Roussy, 114 rue Edouard Vaillant, 94800 Villejuif, France
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