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The most virulent malaria parasite, Plasmodium falciparum, makes use of extensive antigenic diversity to maximise its transmission potential. Parasite genomes contain several highly polymorphic gene families, whose products are the target of protective immune responses. The best studied of these are the PfEMP1 surface proteins, which are encoded by the var multi-gene family and are important virulence factors. During infection, the parasite switches expression between PfEMP1 variants in order to evade adaptive immune responses and prolong infection. On the population level, parasites appear to be structured with respect to their var genes into non-overlapping repertoires, which can lead to high reinfection rates. This non-random structuring of antigenic diversity can also be found at the level of individual var gene repertoires and var genes themselves. However, not much is known about the evolutionary determinants which select for and maintain this structure at different ecological scales. In this thesis I investigate the mechanisms by which multi-scale immune selection and other ecological factors influence the evolution of structured diversity. Using a suite of theoretical frameworks I show that treating diversity as a dynamic property, which emerges from the underlying infection and transmission processes, has a major effect on the relationship between the parasite’s transmis- sion potential and disease prevalence, with important implications for monitoring control efforts. Furthermore, I show that an evolutionary trade-off between within-host and between-host fitness together with functional constraints on diversification can explain the structured diversity found at both the repertoire and parasite population level and might also account for empirically observed exposure-dependent acquisition of immunity. Together, this work highlights the need to consider evolutionary factors acting at different ecological scales to gain a more comprehensive understanding of the complex immune-epidemiology of P. falciparum malaria.

Protozoários do gênero Leishmania são parasitas digenéticos, com uma fase no tubo digestório de um hospedeiro invertebrado (promastigota), e uma fase parasita intracelular de macrófagos (amastigotas). Estudar a demanda de L-arginina no parasita é interessante, uma vez que o aminoácido é indispensável para a sobrevida do parasita e, ao mesmo tempo, serve de substrato para a produção de óxido nítrico, principal composto microbicida dos macrófagos. O objetivo deste trabalho foi caracterizar o transporte de arginina em Leishmania (Leishmania) amazonensis do ponto de vista fisiológico e caracterizar o gene que codifica o transportador do aminoácido, bem como a regulação da sua expressão em resposta a diferentes condições biológicas. Para medir o influxo de L-arginina em fagolisossomos, utilizamos macrófagos J774 infectados com L. (L.) amazonensis e desenvolvemos uma metodologia com citometria de fluxo com sorting para a purificação da organela. Validamos microscopicamente a presença do parasita na organela por sua fluorescência, e avaliamos a integridade da membrana externa dessa com marcador de pH ácido. Paralelamente, o gene que codifica o transportador de arginina do parasita foi caracterizado. Foram encontradas duas cópias em tandem que produzem dois transcritos (5.1AAP3 e 4.7AAP3), cujas regiões 5\'UTR e 3\'UTR são diferentes. Por meio de PCR quantitativo em tempo real, avaliamos a expressão desses transcritos e verificamos que 5.1AAP3 é mais expressa ao longo do desenvolvimento do parasita, com um máximo em fase estacionária. A determinação da meia-vida dos mRNA das duas cópias indicou uma duração de 32,6±5,0min para o mRNA de 4.7AAP3, enquanto que o de 5.1AAP3 não apresentou decaimento até 180min do estudo, evidenciando que a estabilidade maior pode ser a razão de sua maior abundância. A submissão de parasitas à privação de arginina levou a aumento na tomada do aminoácido concomitante ao aumento do transcrito 5.1AAP3. Mutantes nulos de arginase submetidos à privação de arginina respondem com uma taxa de incorporação mais baixa em relação aos parasitas selvagens, e mantém a resposta à privação mesmo com os parasitas em fase estacionária, diferente do observado nos parasitas selvagens. Esse conjunto de resultados nos levou a sugerir que a expressão do transportador pode ser regulada pela estabilidade do mRNA, e que o pool de arginina interno ao parasita pode controlar, num mecanismo de retroalimentação negativo, a expressão de seu transportador. / Protozoan of genus Leishmania are digenetic parasites that present a stage in the life in insect gut (promastigotes) and an intracellular phase (amastigotes) inside vertebrate host macrophages. The study of L-arginine influx consists in an interesting matter, since the amino acid is used on NO production pathway (the main macrophage microbial pathway) but are also important for parasites survival. The aim of this work was to perform a genetic and physiological characterization of the arginine transport in Leishmania (Leishmania) amazonensis. To verify how does the arginine uptake occurs in the phagolisosomes, we used J774 macrophages infected with L. (L.) amazonensis to establish a flow cytometry sorting protocol to purify the organelle. Microscopic validation of organelle integrity was achieved by acidic pH marker treatment and detection of fluorescent parasites. The arginine transporter coding gene was characterized. We found two copies in tandem that produces two transcripts, named 5.1AAP3 and 4.7AAP3, with distinct 5\'UTR and 3\'UTR. By quantitative real time PCR we found that 5.1AAP3 mRNA expression varies along parasite development. This copy was, also, more abundant than 4.7AAP3 mRNA. This last mRNA showed a half-life of 32.6±5.0 min, while the 5.1AAP3 mRNA did not decay until 180min. As response to arginine starvation, wild type parasites increase the uptake of arginine, as well as the abundance of 5.1AAP3 mRNA. Arginase null parasites starvation responses showed lower arginine uptake rates compared to wild type responses. Unlike wild type, the null mutants also respond to starvation in stationary phase. This data set allow us to propose that arginine internal pool can downregulate its transporter expression in a feed-back mechanism.

Toxoplasma gondii est un parasite intracellulaire et obligatoire. Ce protozoa est un des parasites les plus successifs qui infectent tous les animaux à sang chaud, y compris l’humain. Ce succès est probablement à cause de la sécrétion d’une des séries de protéines effectrices, qui sont impliquées dans la modulation des voies de signalisation de la cellule hôte. Cette modulation permet aux parasites d’établir une infection chronique qui dure un long terme, et qui favorise leur transmission à un nouvel hôte. Dans cette étude, nous avons identifié un nouvel effecteur dérivé par la granule dense, appelé GRA18, qui est sécrété dans le cytoplasme de cellule hôte par les tachyzoites intracellulaires. La mutation de gra18 résulte une diminution de virulence chez les parasites de type II, qui suggère l’importance de GRA18 dans la pathogénicité de ce parasite. Afin d’étudier le mécanisme d’action de GRA18, nous avons effectué un criblage à haut-débit d’une librairie humaine chez la levure. Ce criblage nous permet d’identifier β-catenin, GSK3α/β, and PP2A-B56, ce qui sont tous les régulateurs bien connus dans la voie de signalisation canonicale de Wnt. Nous avons confirmé l’intéractome de GRA18 par l’approche biochimique. La surexpression de GRA18 induit l’accumulation de β-catenin dans le noyau de la cellule hôte, aussi que l’induition de gènes régulés par la signalisation de Wnt. Ces effets indiquent GRA18 joue un rôle de régulateur positif de β-catenin. A part de son rôle dans la prolifération, polarisation et la différentiation de cellule, β-catenin est également un facteur de transcription connu pour contrôler la réponse immunitaire et l’inflammation. L’analyse transcriptomique en comparant les macrophages dérivés par la moelle osseuse (BMDM) infectés par le sauvage (WT) et le gra18 mutant parasites confirme un rôle possible de GRA18, la modulation d’expression génique de cellule hôte, surtout ceux qui codent pour les chemokines. Cette régulation est ensuite confirmée par l’ELISA. L’hypothèse possible est que Toxoplasma sécrète GRA18 dans la cellule hôte afin de réguler positivement la production de chemokine reliée à la réponse de Th2, qui par contre atténue la réponse inflammatoire de l’hôte. Cette modulation augmente la chance de dissémination et la persistance de ce parasite par la formation de kyste. / Toxoplasma gondii, the obligate intracellular protozoan parasite, is one of the most successful pathogen that infects virtually all warm-blooded animals including humans. This success of the infection is likely due to its perfect ability to modulate numbers of host signaling pathways through the effector proteins, including those involved in immune responses. This modulation allows the parasite to establish a long-term chronic infection without causing severe symptom in the hosts, which facilitates its transmission to the new hosts. In this study, we identified GRA18, as a novel dense granule derived effector protein that is secreted into the cytoplasm of the host cell by the intracellular tachyzoite. GRA18 deficiency in type II strains attenuated the parasite virulence in mice model, suggesting the importance of GRA18 in the parasite pathogenesis. In order to investigate the mechanism of action of GRA18, we first performed a high-throughput two-hybrid screen of a human library in yeast that led to the identification of β-catenin, GSK3α/β, and PP2A-B56, all which are well known regulators of the canonical Wnt signaling pathway. We then validate the GRA18 interactome by biochemistry approach. The overexpression of GRA18 triggers the accumulation of β-catenin in the host cell nuclei as well as the induction of known canonical β-catenin target genes indicating that GRA18 is acting as a positive regulator of β-catenin. Besides its role in cell proliferation, polarization and differentiation, β-catenin is also a well-known co-transcription factor with important function in the control of inflammation and other immune responses. Transcriptomic analysis comparing mouse bone marrow–derived macrophages infected by wild type and GRA18-dificient parasite confirmed a possible role of GRA18 towards host gene expression and likely those encoding chemokines, which is further confirmed by ELISA experiments. An attractive hypothesis is that Toxoplasma delivers GRA18 to the host cell in order to regulate Th2-related chemoattractant chemokines, which in turn, dampens host inflammatory response leaving more chance for the parasites to disseminate and to cause the long-term persistence by forming the cyst.

Protozoários do gênero Leishmania são parasitas digenéticos, com uma fase no tubo digestório de um hospedeiro invertebrado (promastigota), e uma fase parasita intracelular de macrófagos (amastigotas). Estudar a demanda de L-arginina no parasita é interessante, uma vez que o aminoácido é indispensável para a sobrevida do parasita e, ao mesmo tempo, serve de substrato para a produção de óxido nítrico, principal composto microbicida dos macrófagos. O objetivo deste trabalho foi caracterizar o transporte de arginina em Leishmania (Leishmania) amazonensis do ponto de vista fisiológico e caracterizar o gene que codifica o transportador do aminoácido, bem como a regulação da sua expressão em resposta a diferentes condições biológicas. Para medir o influxo de L-arginina em fagolisossomos, utilizamos macrófagos J774 infectados com L. (L.) amazonensis e desenvolvemos uma metodologia com citometria de fluxo com sorting para a purificação da organela. Validamos microscopicamente a presença do parasita na organela por sua fluorescência, e avaliamos a integridade da membrana externa dessa com marcador de pH ácido. Paralelamente, o gene que codifica o transportador de arginina do parasita foi caracterizado. Foram encontradas duas cópias em tandem que produzem dois transcritos (5.1AAP3 e 4.7AAP3), cujas regiões 5\'UTR e 3\'UTR são diferentes. Por meio de PCR quantitativo em tempo real, avaliamos a expressão desses transcritos e verificamos que 5.1AAP3 é mais expressa ao longo do desenvolvimento do parasita, com um máximo em fase estacionária. A determinação da meia-vida dos mRNA das duas cópias indicou uma duração de 32,6±5,0min para o mRNA de 4.7AAP3, enquanto que o de 5.1AAP3 não apresentou decaimento até 180min do estudo, evidenciando que a estabilidade maior pode ser a razão de sua maior abundância. A submissão de parasitas à privação de arginina levou a aumento na tomada do aminoácido concomitante ao aumento do transcrito 5.1AAP3. Mutantes nulos de arginase submetidos à privação de arginina respondem com uma taxa de incorporação mais baixa em relação aos parasitas selvagens, e mantém a resposta à privação mesmo com os parasitas em fase estacionária, diferente do observado nos parasitas selvagens. Esse conjunto de resultados nos levou a sugerir que a expressão do transportador pode ser regulada pela estabilidade do mRNA, e que o pool de arginina interno ao parasita pode controlar, num mecanismo de retroalimentação negativo, a expressão de seu transportador. / Protozoan of genus Leishmania are digenetic parasites that present a stage in the life in insect gut (promastigotes) and an intracellular phase (amastigotes) inside vertebrate host macrophages. The study of L-arginine influx consists in an interesting matter, since the amino acid is used on NO production pathway (the main macrophage microbial pathway) but are also important for parasites survival. The aim of this work was to perform a genetic and physiological characterization of the arginine transport in Leishmania (Leishmania) amazonensis. To verify how does the arginine uptake occurs in the phagolisosomes, we used J774 macrophages infected with L. (L.) amazonensis to establish a flow cytometry sorting protocol to purify the organelle. Microscopic validation of organelle integrity was achieved by acidic pH marker treatment and detection of fluorescent parasites. The arginine transporter coding gene was characterized. We found two copies in tandem that produces two transcripts, named 5.1AAP3 and 4.7AAP3, with distinct 5\'UTR and 3\'UTR. By quantitative real time PCR we found that 5.1AAP3 mRNA expression varies along parasite development. This copy was, also, more abundant than 4.7AAP3 mRNA. This last mRNA showed a half-life of 32.6±5.0 min, while the 5.1AAP3 mRNA did not decay until 180min. As response to arginine starvation, wild type parasites increase the uptake of arginine, as well as the abundance of 5.1AAP3 mRNA. Arginase null parasites starvation responses showed lower arginine uptake rates compared to wild type responses. Unlike wild type, the null mutants also respond to starvation in stationary phase. This data set allow us to propose that arginine internal pool can downregulate its transporter expression in a feed-back mechanism.

Background: Parasite evolution is hypothesized to select for levels of parasite virulence that maximise transmission success. When host population densities fluctuate, low levels of virulence with limited impact on the host are expected, as this should increase the likelihood of surviving periods of low host density. We examined the effects of Morogoro arenavirus on the survival and recapture probability of multimammate mice (Mastomys natalensis) using a seven-year capture-mark-recapture time series. Mastomys natalensis is the natural host of Morogoro virus and is known for its strong seasonal density fluctuations. Results: Antibody presence was negatively correlated with survival probability (effect size: 5-8% per month depending on season) but positively with recapture probability (effect size: 8%). Conclusions: The small negative correlation between host survival probability and antibody presence suggests that either the virus has a negative effect on host condition, or that hosts with lower survival probability are more likely to obtain Morogoro virus infection, for example due to particular behavioural or immunological traits. The latter hypothesis is supported by the positive correlation between antibody status and recapture probability which suggests that risky behaviour might increase the probability of becoming infected.

Chez les vertébrés, la réponse immunitaire acquise représente un mécanisme sophistiqué de réponse face aux parasites dont l‟une des particularités est la possibilité qu‟il offre aux mères de transférer certains de ses effecteurs à leurs nouveau-nés. Pourtant, malgré un intérêt croissant pour les effets maternels, les déterminants écologiques et évolutifs du transfert d‟anticorps maternels n‟ont pas encore été beaucoup étudiés. L‟analyse d‟un cadre théorique spécialement développé pour inclure le transfert transgénérationnel d‟immunité montre que l‟évolution de la capacité à transférer une immunité temporaire aux jeunes dépend des caractéristiques de l‟hôte et du parasite. En particulier, l‟augmentation de l‟espérance de vie de l‟hôte favorise l‟évolution de réponses immunitaires acquises, et la protection conférée par ces réponses est aussi supposée durer plus longtemps chez les hôtes longévifs. En accord avec cette prédiction, une étude de vaccination transgénérationnelle chez une espèce d‟oiseau de mer longévive a permis de mettre en évidence une demi-vie des anticorps maternels particulièrement longue. Les conditions sociales sont aussi un élément clé, et chez une espèce de mammifère, j‟ai pu montrer qu‟elles permettent un élargissement du répertoire d‟anticorps maternels. Le transfert d‟anticorps maternels est aussi à même de modifier les dynamiques épidémiologiques et pourrait présenter un atout non négligeable si la vaccination était utilisée en conservation. Enfin, ce mécanisme pourrait être mis à profit pour estimer l‟exposition des mères, et ainsi inférer la dispersion entre différentes zones d‟habitat / In vertebrate species, acquired immune response represents a sophisticated protection mechanism against parasites that has the particularity of enabling mothers to transmit part of its effectors to their newborns. Yet, despite an increasing interest in maternal effects, ecological and evolutionary determinants of the transfer of maternal antibodies remain poorly studied. The analysis of a theoretical framework specially developed to include a transgenerational transfer of immunity show that the evolution of an ability to temporarily protect offspring depends on the characteristics of both the host and the parasite. In particular, increasing the life span of the host favors the evolution of acquired immune responses and increases the duration of the protection offered by these mechanisms. Accordingly, a transgenerational vaccination study in a long-lived seabird revealed a particularly long half-life of maternal antibodies. Social conditions also proved important in a mammal species as they can allow for the broadening of the repertoire covered by maternal antibodies. The transfer of maternal antibodies could also modify epidemiological dynamics and could bbe an interesting asset if vaccination was used as a conservation tool. Finally, this mechanism could be used to estimate the exposure of mother and thus infer the dispersal rate between different habitat patches.

京都大学 / 0048 / 新制・課程博士 / 博士(人間・環境学) / 甲第18605号 / 人博第701号 / 新制||人||167(附属図書館) / 26||人博||701(吉田南総合図書館) / 31505 / 京都大学大学院人間・環境学研究科相関環境学専攻 / (主査)教授 加藤 眞, 教授 市岡 孝朗, 教授 瀬戸口 浩彰, 教授 宮本 嘉久, 教授 新宮 一成 / 学位規則第4条第1項該当 / Doctor of Human and Environmental Studies / Kyoto University / DGAM

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La compréhension du processus d’adaptation des populations de parasites à leur plante-hôte est une question fondamentale en écologie évolutive. C’est également un enjeu majeur de recherche finalisée qui a des retombées pour la protection des cultures. L’oomycète Plasmopara viticola, agent causal du mildiou de la vigne, attaque les espèces du genre Vitis. Dans un contexte où l’enjeu principal des programmes d’amélioration est la durabilité des résistances, des connaissances nouvelles sur l’écologie et l’évolution de l'interaction entre le parasite et son hôte sont nécessaires afin d’évaluer le potentiel du mildiou à surmonter ces résistances. Dans ma thèse, je me suis intéressée au rôle de la plante-hôte comme facteur d’évolution des populations de mildiou, en posant cette question à différentes échelles évolutives : (i) dans le bassin d’origine du pathogène (Amérique du Nord), j’ai cherché à évaluer le degré de spécialisation du parasite sur sa gamme d’hôtes sauvages et cultivés; (ii) en Europe, où le mildiou de la vigne a été introduit récemment, j’ai étudié l’évolution des populations de mildiou soumis à la pression de sélection des résistances des nouvelles variétés de vigne. Pour comprendre la spécialisation plante-hôte dans ce pathosystème où plusieurs espèces cryptiques ont été identifiées, nous avons réalisé des tests d’inoculations croisées entre espèces hôtes (Vitis spp.) et agent pathogène (P. viticola). Les données phénotypiques et morphologiques apportent les preuves d’une spécialisation plante-hôte au sein des populations de P. viticola : les espèces A et D de mildiou sont spécialisées sur leur plante-hôte, tandis que le processus de spécialisation est en cours pour les espèces B et C. Même si aucune différenciation génétique n’a été montrée au sein de l’espèce C, il existe deux groupes distincts au sein de l’espèce B. Les isolats du compartiment cultivé sont en moyenne plus agressifs que les isolats issus des vignes sauvages, indiquant une adaptation des isolats cultivés sur leur plante hôte. A partir d’un large échantillonnage, nous avons étudié la distribution des espèces de mildiou sur leurs plantes-hôtes sauvages et cultivées. Ce travail a permis d’identifier une nouvelle espèce cryptique et a confirmé la spécialisation plante-hôte. En Europe, nos résultats montrent que le déploiement limité de variétés à résistantes partielles a conduit à des modifications des populations de mildiou: apparition d’isolats virulents (i.e. contournant un QTL majeur de résistance), et augmentation de l’agressivité sur Vitis vinifera. Dans le but de comprendre les mécanismes à l’origine de la spécialisation et du contournement des résistances, nous nous sommes intéressés au répertoire d’effecteurs du parasite. Une centaine d’effecteurs candidats ont été identifiés en utilisant les données disponibles sur le génome de P. viticola. L’analyse du polymorphisme de 32 candidats sur une sélection d’isolats montre que trois d’entre eux évoluent sous sélection positive. Ces résultats soulignent l’importance de la plante-hôte comme facteur de diversification des populations de l’agent pathogène et révèlent que le mildiou s’adapte rapidement aux résistances de la vigne. Il est désormais nécessaire de mieux appréhender le déploiement des résistances de la vigne afin qu’elles puissent être durables. / Understanding the process of adaptation of parasite populations to their host-plant is a key issue in evolutionary ecology. It is also a major subject in applied research that has implications for crop protection. The oomycete Plasmopara viticola, the causal agent of downy mildew, attacks the species of the Vitis genus. In a context where the main concern of the breeding programs is the durability of resistance, new knowledge about the ecology and evolution of the interaction between parasite and host is needed in order to evaluate the potential of downy mildew to overcome the resistance. In my thesis, I addressed the role of the host-plant as an evolutionary factor for downy mildew populations, by asking this question at two different evolutionary scales: (i) in the pathogen region of origin (North America) I assessed the degree of specialization of the parasite on its wild and cultivated host range (ii) in Europe, where downy mildew has been introduced recently, I studied the evolution of downy mildew populations subject to the selection pressure imposed by resistant grapevine varieties. To understand the host-plant specialization in this pathosystem, where several cryptic species have been identified, we performed cross inoculations between different host (Vitis spp.) and pathogen (P. viticola) species. Morphological and phenotypic data provide evidence of host-plant specialization in P. viticola populations: downy mildew species A and D are specialized on their host-plant, while the specialization process is ongoing for species B and C. Although no genetic differentiation has been shown inside species C, there are two distinct groups within species B. Isolates from the cultivated compartment are on average more aggressive than isolates from wild vines, indicating an adaptation of isolates growing on cultivated host-plants. Finally, a large-scale study of the distribution of downy mildew species on both their wild and cultivated host-plants resulted in the identification of a new cryptic species and confirmed the host-plant specialization. In Europe, our results show that the limited deployment of resistant varieties has led to changes in downy mildew populations: emergence of virulent isolates (i.e. breakdown of a major QTL for resistance), and increased aggressiveness on Vitis vinifera. In order to understand the mechanisms at the origin of specialization and resistance breakdown, we examined the parasite’s effector repertoire. Over one hundred effector candidates were identified using available data on the P. viticola genome. The polymorphism of 32 candidate genes revealed that three of them evolve under positive selection. Our results reveal the strong ability of downy mildew to adapt to its host plant and to plant resistance. They should be taken into account when devising strategies for the deployment of grapevine resistances in order to guarantee their durability.