Cytonuclear interactions remain stable during allopolyploid evolution despite repeated whole-genome duplications in Brassica

Several plastid macromolecular protein complexes are encoded by both nuclear and plastid genes. Therefore, cytonuclear interactions are held in place to prevent genomic conflicts that may lead to incompatibilities. Allopolyploidy resulting from hybridization and genome doubling of two divergent species can disrupt these fine-tuned interactions, as newly formed allopolyploid species confront biparental nuclear chromosomes with a uniparentally inherited plastid genome. To avoid any deleterious effects of unequal genome inheritance, preferential transcription of the plastid donor over the other donor has been hypothesized to occur in allopolyploids. We used Brassica as a model to study the effects of paleopolyploidy in diploid parental species, as well as the effects of recent and ancient allopolyploidy in Brassica napus, on genes implicated in plastid protein complexes. We first identified redundant nuclear copies involved in those complexes. Compared with cytosolic protein complexes and with genome-wide retention rates, genes involved in plastid protein complexes show a higher retention of genes in duplicated and triplicated copies. Those redundant copies are functional and are undergoing strong purifying selection. We then compared transcription patterns and sequences of those redundant gene copies between resynthesized allopolyploids and their diploid parents. The neopolyploids showed no biased subgenome expression or maternal homogenization via gene conversion, despite the presence of some non-synonymous substitutions between plastid genomes of parental progenitors. Instead, subgenome dominance was observed regardless of the maternal progenitor. Our results provide new insights on the evolution of plastid protein complexes that could be tested and generalized in other allopolyploid species

Genome sequence of the stramenopile Blastocystis, a human anaerobic parasite

International audienceABSTRACT: BACKGROUND: Blastocystis is a highly prevalent anaerobic eukaryotic parasite of humans and animals that is associated with various gastrointestinal and extraintestinal disorders. Epidemiological studies have identified different subtypes but no one subtype has been definitively correlated with disease. RESULTS: Here we report the 18.8 Mb genome sequence of a Blastocystis subtype 7 isolate, which is the smallest stramenopile genome sequenced to date. The genome is highly compact and contains intriguing rearrangements. Comparisons with other available stramenopile genomes (plant pathogenic oomycete and diatom genomes) revealed effector proteins potentially involved in the adaptation to the intestinal environment, which were likely acquired via horizontal gene transfer. Moreover, Blastocystis living in anaerobic conditions harbors mitochondria-like organelles. An incomplete oxidative phosphorylation chain, a partial Krebs cycle, amino acid and fatty acid metabolisms and an iron-sulfur cluster assembly are all predicted to occur in these organelles. Predicted secretory proteins possess putative activities that may alter host physiology, such as proteases, protease-inhibitors, immunophilins and glycosyltransferases. This parasite also possesses the enzymatic machinery to tolerate oxidative bursts resulting from its own metabolism or induced by the host immune system. CONCLUSIONS: This study provides insights into the genome architecture of this unusual stramenopile. It also proposes candidate genes with which to study the physiopathology of this parasite and thus may lead to further investigations into Blastocystis-host interactions

Thymus‐derived regulatory T cells restrain pro‐inflammatory Th1 responses by downregulating CD

The severity and intensity of autoimmune disease in Immune dysregulation, polyendocrinopathy, enteropathy, X-linked (IPEX) patients and in scurfy mice emphasizes the critical role played by thymus-derived regulatory T cells (tTregs) in maintaining peripheral immune tolerance. However, although tTregs are critical to prevent lethal autoimmunity and excessive inflammatory responses, their suppressive mechanism remains elusive. Here we demonstrate that tTregs selectively inhibit CD27/CD70-dependent Th1 priming, while leaving the IL-12-dependent pathway unaffected. Immunized mice depleted of tTregs showed an increased response of IFN-γ-secreting CD4+ T cells that was strictly reliant on a functional CD27/CD70 pathway. In vitro studies revealed that tTregs downregulate CD70 from the plasma membrane of dendritic cells (DCs) in a CD27-dependent manner. CD70 downregulation required contact between Tregs and DCs and resulted in endocytosis of CD27 and CD70 into the DC. These findings reveal a novel mechanism by which tTregs can maintain tolerance or prevent excessive, proinflammatory Th1 responsesin pressSCOPUS: ar.jFLWINinfo:eu-repo/semantics/publishe

The streamlined genome of Phytomonas spp. relative to human pathogenic kinetoplastids reveals a parasite tailored for plants

Members of the family Trypanosomatidae infect many organisms, including animals, plants and humans. Plant-infecting trypanosomes are grouped under the single genus Phytomonas, failing to reflect the wide biological and pathological diversity of these protists. While some Phytomonas spp. multiply in the latex of plants, or in fruit or seeds without apparent pathogenicity, others colonize the phloem sap and afflict plants of substantial economic value, including the coffee tree, coconut and oil palms. Plant trypanosomes have not been studied extensively at the genome level, a major gap in understanding and controlling pathogenesis. We describe the genome sequences of two plant trypanosomatids, one pathogenic isolate from a Guianan coconut and one non-symptomatic isolate from Euphorbia collected in France. Although these parasites have extremely distinct pathogenic impacts, very few genes are unique to either, with the vast majority of genes shared by both isolates. Significantly, both Phytomonas spp. genomes consist essentially of single copy genes for the bulk of their metabolic enzymes, whereas other trypanosomatids e.g. Leishmania and Trypanosoma possess multiple paralogous genes or families. Indeed, comparison with other trypanosomatid genomes revealed a highly streamlined genome, encoding for a minimized metabolic system while conserving the major pathways, and with retention of a full complement of endomembrane organelles, but with no evidence for functional complexity. Identification of the metabolic genes of Phytomonas provides opportunities for establishing in vitro culturing of these fastidious parasites and new tools for the control of agricultural plant disease. © 2014 Porcel et al

Study of molecular and cellular mechanisms involved in regulatory T cell suppressive activity

La réponse immune représente une réponse complexe à laquelle correspond une succession d’événements orchestrés finement. Parmi les mécanismes qui régulent la réponse immune, les lymphocytes T régulateurs (Tregs) assurent le maintien de la tolérance en périphérie et le contrôle des réponses immunes adaptatives. Ils représentent une population hétérogène et leurs mécanismes de suppression sont toujours l’objet d’intenses recherches. Suivant le contexte de suppression et leur nature, les lymphocytes Tregs réalisent une inhibition de l’activation des lymphocytes Th, soit directement, soit via la modulation de la fonction des cellules dendritiques (DC). Dans un modèle d’immunisation par des cellules dendritiques chargées de KLH, les lymphocytes Tregs naturels contrôlent sélectivement l’initiation des réponses de type Th1/CTL spécifiques de l’antigène. Le but de ce travail était de définir quels sont les acteurs potentiels du contrôle de cette réponse. A l’aide de l’anticorps PC61 dirigé contre le récepteur CD25 et éliminant les lymphocytes Tregs naturels, nous avons montré que le ligand de costimulation CD70 joue un rôle clé dans leur régulation de la réponse Th1/CTL (Article 1). Ainsi, dans des conditions normales, la cytokine IL-12 induit principalement l’initiation de la réponse Th1 in vivo, tandis qu’en l’absence de lymphocytes Tregs naturels, la voie CD70/CD27 est une voie alternative d’induction de l’IFN-γ. Cette voie d’activation pourrait être opérationnelle dans certains contextes infectieux lorsque les lymphocytes Tregs sont déstabilisés voire éliminés, par exemple lors d’infections par Toxoplasma gondii ou par les virus HTLV1, SIV ou HIV. Nous avons montré que les lymphocytes Tregs naturels diminuent l’expression du ligand CD70 sur les DC, de manière dépendante de son récepteur CD27. Ensuite, nous nous sommes intéressés à une deuxième population de lymphocytes T régulateurs, les lymphocytes Tregs ICOShigh induits in vivo par le traitement avec l’anticorps anti-CTLA-4. Dans le cadre d’une colite induite par l’agent alkylant TNBS et mettant en jeu une réponse Th1, cette population de lymphocytes Tregs amplifiée par le traitement à l’anticorps anti-CTLA-4 régule la réponse immune via la cytokine anti-inflammatoire IL-10 et l’enzyme immunosuppressive IDO (Article 2). Ainsi, les résultats obtenus nous ont permis de répondre à notre objectif et de définir certains mécanismes de suppression des lymphocytes Tregs naturels et des lymphocytes Tregs induits. Dans la dernière partie de ce travail, nous avons cherché à comparer les populations de lymphocytes Tregs naturels et ICOShigh présentes dans l’intestin d’une souris naïve. Une analyse transcriptomique a révélé que ces deux populations s’opposent sur les plans phénotypique et fonctionnel. Nous proposons un modèle dans lequel les deux populations de lymphocytes Tregs agiraient en synergie pour maintenir l’homéostasie intestinale. Les lymphocytes Tregs ICOShigh différenciés au niveau local et continuellement activés contrôleraient la réponse inflammatoire associée à la présence de la flore commensale. Les lymphocytes Tregs naturels, en quiescence dans les ganglions mésentériques, n’interviendraient qu’en cas d’infection par des pathogènes.L’étude des lymphocytes T régulateurs soulève un certain nombre de concepts clés de l’immunité :la spécificité des réponses, la distinction des microorganismes commensaux et pathogènes… Mieux connaître les lymphocytes Tregs dans un modèle murin permettra de mieux comprendre les réponses inflammatoires intestinales chroniques observées chez l'homme et d’envisager, à terme, de nouveaux traitements./An immune response is complex and implies numerous sequential events. It is regulated by different mechanisms, among which regulatory T cells maintain peripheral tolerance and control adaptive immune responses. Regulatory T cells are very heterogeneous and suppress immune responses through different mechanisms, still under investigation. They can inhibit T cell activation directly or through the modulation of dendritic cell function, depending on their nature and the tissular context.In a dendritic cell-mediated immunization model, naturally occurring regulatory T cells selectively control the priming of antigen-specific Th1/CTL responses. Our goal was to define the potential actors of this control, targeted by natural regulatory T cells. Using the PC61 antibody which targets and depletes these cells, we showed that the costimulation ligand CD70 plays a key role in their control of Th1/CTL responses (first article). We showed that mainly IL-12 provokes Th1 development in normal conditions, wheras CD70 plays a major role in priming Th1 responses in the absence of natural Tregs. This pathway can be operational if regulatory T cells are destabilized or even depleted, for example during infection with Toxoplasma gondii or with HTLV1, SIV or HIV. We showed that natural Tregs downregulate CD70 expression on the surface of DCs.Next, we focused on another regulatory T cell population, induced in vivo by the anti-CTLA-4 mAb treatment. In a model of pro-Th1 colitis, induced by the alkylating agent TNBS, these ICOShigh regulatory T cells exert an IL-10 and IDO-dependant control over the immune response (second article). Thus, we succeeded in determining some control mechanisms of the immune response targeted by two populations of regulatory T cells.Finally, we compared two regulatory T cell populations: naturally occurring regulatory T cells and ICOShigh regulatory T cells from the intestines of naïve mice. A transcriptional analysis revealed two populations phenotypically and functionally distinct. We proposed a model in which these populations act synergistically and both maintain intestinal homeostasis. ICOShigh regulatory T cells might control commensal gut flora-specific inflammatory responses and quiescent natural regulatory T cells from mesenteric lymph nodes might control potential pathogen infections.As a conclusion, this study raises some immunological issues: specificity of immune responses, distinction between commensal and pathogenic microorganisms… A better knowledge of these regulatory populations will lead to a better understanding of human intestinal responses and in the medium term will lead to new therapeutic approaches and tools.Doctorat en Sciencesinfo:eu-repo/semantics/nonPublishe

Study of molecular and cellular mechanisms involved in regulatory T cell suppressive activity

La réponse immune représente une réponse complexe à laquelle correspond une succession d’événements orchestrés finement. Parmi les mécanismes qui régulent la réponse immune, les lymphocytes T régulateurs (Tregs) assurent le maintien de la tolérance en périphérie et le contrôle des réponses immunes adaptatives. Ils représentent une population hétérogène et leurs mécanismes de suppression sont toujours l’objet d’intenses recherches. Suivant le contexte de suppression et leur nature, les lymphocytes Tregs réalisent une inhibition de l’activation des lymphocytes Th, soit directement, soit via la modulation de la fonction des cellules dendritiques (DC). Dans un modèle d’immunisation par des cellules dendritiques chargées de KLH, les lymphocytes Tregs naturels contrôlent sélectivement l’initiation des réponses de type Th1/CTL spécifiques de l’antigène. Le but de ce travail était de définir quels sont les acteurs potentiels du contrôle de cette réponse. A l’aide de l’anticorps PC61 dirigé contre le récepteur CD25 et éliminant les lymphocytes Tregs naturels, nous avons montré que le ligand de costimulation CD70 joue un rôle clé dans leur régulation de la réponse Th1/CTL (Article 1). Ainsi, dans des conditions normales, la cytokine IL-12 induit principalement l’initiation de la réponse Th1 in vivo, tandis qu’en l’absence de lymphocytes Tregs naturels, la voie CD70/CD27 est une voie alternative d’induction de l’IFN-γ. Cette voie d’activation pourrait être opérationnelle dans certains contextes infectieux lorsque les lymphocytes Tregs sont déstabilisés voire éliminés, par exemple lors d’infections par Toxoplasma gondii ou par les virus HTLV1, SIV ou HIV. Nous avons montré que les lymphocytes Tregs naturels diminuent l’expression du ligand CD70 sur les DC, de manière dépendante de son récepteur CD27. Ensuite, nous nous sommes intéressés à une deuxième population de lymphocytes T régulateurs, les lymphocytes Tregs ICOShigh induits in vivo par le traitement avec l’anticorps anti-CTLA-4. Dans le cadre d’une colite induite par l’agent alkylant TNBS et mettant en jeu une réponse Th1, cette population de lymphocytes Tregs amplifiée par le traitement à l’anticorps anti-CTLA-4 régule la réponse immune via la cytokine anti-inflammatoire IL-10 et l’enzyme immunosuppressive IDO (Article 2). Ainsi, les résultats obtenus nous ont permis de répondre à notre objectif et de définir certains mécanismes de suppression des lymphocytes Tregs naturels et des lymphocytes Tregs induits. Dans la dernière partie de ce travail, nous avons cherché à comparer les populations de lymphocytes Tregs naturels et ICOShigh présentes dans l’intestin d’une souris naïve. Une analyse transcriptomique a révélé que ces deux populations s’opposent sur les plans phénotypique et fonctionnel. Nous proposons un modèle dans lequel les deux populations de lymphocytes Tregs agiraient en synergie pour maintenir l’homéostasie intestinale. Les lymphocytes Tregs ICOShigh différenciés au niveau local et continuellement activés contrôleraient la réponse inflammatoire associée à la présence de la flore commensale. Les lymphocytes Tregs naturels, en quiescence dans les ganglions mésentériques, n’interviendraient qu’en cas d’infection par des pathogènes.L’étude des lymphocytes T régulateurs soulève un certain nombre de concepts clés de l’immunité :la spécificité des réponses, la distinction des microorganismes commensaux et pathogènes… Mieux connaître les lymphocytes Tregs dans un modèle murin permettra de mieux comprendre les réponses inflammatoires intestinales chroniques observées chez l'homme et d’envisager, à terme, de nouveaux traitements./An immune response is complex and implies numerous sequential events. It is regulated by different mechanisms, among which regulatory T cells maintain peripheral tolerance and control adaptive immune responses. Regulatory T cells are very heterogeneous and suppress immune responses through different mechanisms, still under investigation. They can inhibit T cell activation directly or through the modulation of dendritic cell function, depending on their nature and the tissular context.In a dendritic cell-mediated immunization model, naturally occurring regulatory T cells selectively control the priming of antigen-specific Th1/CTL responses. Our goal was to define the potential actors of this control, targeted by natural regulatory T cells. Using the PC61 antibody which targets and depletes these cells, we showed that the costimulation ligand CD70 plays a key role in their control of Th1/CTL responses (first article). We showed that mainly IL-12 provokes Th1 development in normal conditions, wheras CD70 plays a major role in priming Th1 responses in the absence of natural Tregs. This pathway can be operational if regulatory T cells are destabilized or even depleted, for example during infection with Toxoplasma gondii or with HTLV1, SIV or HIV. We showed that natural Tregs downregulate CD70 expression on the surface of DCs.Next, we focused on another regulatory T cell population, induced in vivo by the anti-CTLA-4 mAb treatment. In a model of pro-Th1 colitis, induced by the alkylating agent TNBS, these ICOShigh regulatory T cells exert an IL-10 and IDO-dependant control over the immune response (second article). Thus, we succeeded in determining some control mechanisms of the immune response targeted by two populations of regulatory T cells.Finally, we compared two regulatory T cell populations: naturally occurring regulatory T cells and ICOShigh regulatory T cells from the intestines of naïve mice. A transcriptional analysis revealed two populations phenotypically and functionally distinct. We proposed a model in which these populations act synergistically and both maintain intestinal homeostasis. ICOShigh regulatory T cells might control commensal gut flora-specific inflammatory responses and quiescent natural regulatory T cells from mesenteric lymph nodes might control potential pathogen infections.As a conclusion, this study raises some immunological issues: specificity of immune responses, distinction between commensal and pathogenic microorganisms… A better knowledge of these regulatory populations will lead to a better understanding of human intestinal responses and in the medium term will lead to new therapeutic approaches and tools.Doctorat en Sciencesinfo:eu-repo/semantics/nonPublishe

Role of CD27/CD70 pathway of activation in immunity and tolerance.

The CD70/CD27 axis has gained increasing interest among the immunologists, because of its capacity to regulate immunity versus tolerance. Recent studies clearly show that expression of CD70 may prevent tolerance induced by antigen presentation in the steady-state, i.e. by nonactivated DCs. In addition, CD27 signaling appears critical for T cell expansion and survival and therefore, induction of long-term memory. It contributes to germinal center formation, B cell activation, and production of neutralizing antibodies but can also be subverted by viruses, in particular, during chronic infections. The potential role of the CD27/CD70 pathway in the course of inflammatory diseases, as in EAE, arthritis, and inflammatory bowel disease models, suggests that CD70 may be a target for immune intervention. Conversely, the potency of costimulation through CD27 suggests that the CD27/CD70 axis could be exploited for the design of anti-cancer vaccines.Comparative StudyJournal ArticleResearch Support, Non-U.S. Gov'tReviewSCOPUS: sh.jinfo:eu-repo/semantics/publishe

Etude des mécanismes cellulaires et moléculaires impliqués dans la fonction suppressive des lymphocytes T régulateurs

PARIS5-BU Cordeliers (751062101) / SudocSudocFranceF