Le virus de la panachure jaune du riz (virus RYMV pour Rice Yellow Mottle Virus) infecte principalement le genre Oryza et provoque d'importants dégâts sur les cultures de riz en Afrique. Bien que son génome soit rudimentaire, ce virus code des protéines essentielles pour son maintien chez l’hôte en dépit des mécanismes de défense de la plante. Les travaux récents de l’équipe ont permis d’identifier la protéine P1 codée par ce virus comme une protéine qui pourrait, grâce à sa propriété de suppresseur de RNA silencing, permettre au virus de contourner un mécanisme de défense essentiel de l’hôte et permettre au virus de perpétuer son cycle viral. Peu de données concernant les mécanismes d’action de la protéine P1 sont disponibles à ce jour. Le travail entrepris au cours de ma thèse a donc consisté à compléter les connaissances sur la biochimie de cette protéine, à définir sa structure tridimensionnelle et à mettre à jour sa localisation sub cellulaire afin de révéler des propriétés qui pourraient nous permettre non seulement de mieux comprendre comment cette protéine opère ses fonctions mais également de définir des méthodes de lutte adéquates contre ce virus. Ainsi, je montre que la protéine P1 constitue une nouvelle famille de protéine à doigt de zinc possédant une structure 3D inédite composée d’un premier domaine impliqué dans la dimérisation de la protéine et dans des interactions avec des ligands dont certains pourraient provenir de la plante hôte. Mon travail permet également d’identifier un deuxième domaine senseur de l’état redox au sein de la protéine qui lui permet probablement de sonder l’état de la plante pendant l’infection virale et d’adapter ses conformations pour assurer ses fonctions. Finalement, une approche par mutagénèse sur la protéine P1 assistée par la nouvelle structure 3D démontre qu’il est désormais possible d’identifier les résidus essentiels à la protéine pour sa participation dans l’infection virale. Ce travail ouvre donc de nombreuses perspectives pour de futures études de mécanistique sur ces domaines-clé de la protéine, ainsi que pour des études sur sa diversité génétique au sein des très nombreux isolats du virus RYMV en Afrique. / The virus of rice yellow mottle virus (RYMV for Rice Yellow Mottle Virus) mainly infects the genus Oryza and causes significant damage to rice crops in Africa. Although its genome is rudimentary, this virus code essential proteins for its maintenance in the host despite the defense mechanisms of the plant. Recent work by the team has identified the P1 protein encoded by the virus as a protein that could, through its ownership of RNA silencing suppressor, allow the virus to bypass an essential defense mechanism of the host and allow the virus to perpetuate its viral cycle. Little data on the mechanisms of action of the P1 protein is available to date. The work undertaken during my thesis was therefore to supplement the knowledge of the biochemistry of this protein, to define its three-dimensional structure and update its sub cellular localization to reveal properties that could enable us not only to understand how this protein works its functions but also to define methods of adequate response against the virus. Thus, I show that the P1 protein is a new zinc finger protein family having a unique 3D structure consisting of a first domain involved in the dimerization of the protein and in interactions with ligands some of which may originate from the plant host. My work also identifies a second sensor field in the redox state of the protein that probably allows him to probe the state of the plant during viral infection and adapt its conformation to conduct their duties. Finally, a mutagenesis approach to P1 assisted by the new 3D protein structure shows that it is now possible to identify critical residues in the protein for its participation in the viral infection. This work thus opens up many possibilities for future mechanistic studies on these key areas of the protein, as well as for studies of genetic diversity within many RYMV isolates of virus in Africa

Parapoxvirus ovis (PPVO) is known for its immunostimulatory capacities and has been successfully used to generate vector vaccines effective especially in non-permissive host species. Murine conventional and plasmacytoid dendritic cells (cDC and pDC) are able to recognize PPVO. The PPVO-sensing receptor on pDC is hitherto unknown. In this study we aimed to define the pattern recognition receptor responsible for the activation of murine pDC by inactivated and replication-competent PPVO. We show that PPVO-induced expression of type I and type III interferons, pro-inflammatory cytokines, and costimulatory CD86 by bone marrow-derived pDC but not cDC is blocked by chloroquine, an inhibitor of endosomal maturation. The activation of pDC is independent of viral replication and depends mainly on TLR9. Moreover, the use of phosphatidylinositol 3-kinase inhibitor wortmannin or C-Jun-N-terminal kinase inhibitor SP600125 results in significant reduction of PPVO-induced pDC activation. Taken together, our data identify endosomal TLR9 as PPVO-sensing receptor in pDC.

La pneumonie est la première cause de mortalité chez l’enfant dans le monde. Elle peut être provoquée par un certain nombre d’agents pathogènes connus mais 15 à 35% des pneumonies de l’enfant restent encore non renseignées d’un point de vue étiologique. L’utilisation d’un test moléculaire de découverte de nouveaux pathogènes nous a permis de découvrir de nouvelles espèces de Torque Teno Mini Virus (TTMV, Anelloviridae), nommées TTMV-LY, dans trois épanchements pleuraux provenant d’enfants hospitalisés avec une pleuro-pneumopathie, dont l’étiologie demeurait inconnue. Les TTMV sont des virus ubiquitaires dont l’implication dans une pathologie reste à déterminer. Les voies respiratoires ayant précédemment été décrites pour être un site d'infection des anellovirus, nous avons entrepris de caractériser ces nouveaux virus, ainsi que d’étudier leur potentiel rôle dans la pathogénèse.Les génomes complets de TTMV-LY ont été isolés, caractérisés puis répliqués in vitro. La réponse des cellules épithéliales alvéolaires, ainsi que des cellules présentatrices d’antigènes (CPA), impliquées dans l’inflammation, a été étudiée après infection par les virions néo-synthétisés.Ces travaux ont démontré que : i) les TTMV-LY peuvent coloniser les poumons en profondeur, ii) les cellules pulmonaires sont permissives aux TTMV-LY et permettent une réplication virale efficace, iii) l’infection virale module les réponses cellulaires et immunitaires des cellules pulmonaires en induisant des dérégulations de l’expression génique et la production de médiateurs inflammatoires, iv) les TTMV-LY seraient capables d’interagir avec les CPA et de réguler ainsi différentiellement le processus inflammatoire.L’ensemble de ces résultats ont permis de mettre en évidence une implication potentielle des TTMV-LY dans la pathogénèse des pneumopathies, et souligné la complexité des mécanismes biologiques mis en jeu lors de l’infection par les virus de cette famille. / Pneumonia is the leading cause of death in children worldwide. It can be caused by a number of known pathogens, but 15-35% of childhood pneumonia are still not associated with an etiologic agent. A pathogen discovery assay allowed us to identify new species of Torque Teno Mini Virus (TTMV, Anelloviridae), named TTMV-LY, in three undiagnosed pleural effusions from children hospitalized with parapneumonic empyema. TTMV are ubiquitous orphan viruses, and their involvement in pathogenesis remains unknown. The respiratory tract was previously described to be a site of anellovirus detection. We investigated the role of these new species in the pathogenesis of severe pneumonia.Full-length TTMV-LY genomes were isolated and in vitro replicated. The response of alveolar epithelial cells, and antigen presenting cells (APC), both involved in the inflammation process, was studied after infection with neo-synthesized virions.This study showed for the first time that: i) TTMV-LY can deeply colonize lungs, ii) alveolar epithelial cells are permissive to the TTMV-LY and allow an efficient replication, iii) viral infection modulates cellular and innate immune responses of alveolar epithelial cells, by inducing gene expression deregulations and inflammatory mediators production, iv) TTMV-LY are able to interact with APC and thereby regulate differentially their inflammatory process.All these results allowed to highlight a potential involvement of TTMV-LY in the pathogenesis of severe pneumonia and brought out the complexity of the biological mechanisms taking place during infection by viruses of this family.

Estima-se que 170 milhões de pessoas no mundo estejam infectadas com o vírus da hepatite C (VHC), o que está altamente relacionado à ocorrência de hepatite crônica e carcinoma hepatocelular. A prevalência de esteatose hepática em doentes com hepatite C crônica é muito maior do que na população geral variando entre 40 a 75%. A associação entre a infecção pelo VHC e esteatose hepática é multifatorial. Duas formas de esteatose hepática são encontradas em pacientes com hepatite C crônica: esteatose metabólica (fatores de risco) e citopática relacionada ao genótipo 3a. Os lipídios são essenciais para o ciclo de replicação do VHC, eles podem exercer seu efeito em diferentes níveis como: grupos prostéticos em proteínas virais e/ou cofatores celulares na replicação de VHC, componentes especializados na estrutura do VHC onde ocorre a replicação ou como constituinte das partículas lipovirais. Trabalhos experimentais realizados anteriormente por nosso grupo relataram que a administração do composto natural Yo Jyo Hen Shi Ko (YHK) promove a inibição do desenvolvimento da esteatose, redução dos marcadores de estresse oxidativo, menor escore de inflamação, melhora nas concentrações de aminotransferases e diminuição da gordura visceral em um modelo animal de esteato-hepatite não alcoólica. A terapia padrão da hepatite C consiste em uma combinação de interferon peguilado alfa (PEG-IFN-alfa) que estimula o sistema imunológico do hospedeiro para combater a infecção e o composto antiviral ribavirina. Atualmente foram aprovados pelas agências de saúde os inibidores de protease Boceprevir, Telaprevir, Daclatasvir e Simeprevir. No entanto, sua eficiência varia entre os genótipos e as constantes mutações do vírus podem levar a resistência. A falta de uma vacina ou uma terapia definitiva faz com que diversos compostos com diferentes mecanismos de ação sejam testados como possíveis alternativas de tratamento. Tendo em vista a capacidade do YHK de reduzir a esteatose e a importância do metabolismo para a replicação do VHC, o objetivo deste trabalho foi avaliar o efeito do YHK no ciclo celular do VHC. Para isso foram utilizadas técnicas de cultura celular que permitem o estudo das diferenças fases do ciclo de replicação do VHC: entrada (VHCpp), replicação - replicons JFH1-NS3-5B e Con1, replicação e infecção- JC1-Fluc. De forma a elucidar a possibilidade de um único componente da fórmula YHK apresentar efeito sobre o VHC, foram utilizadas para comparação as substâncias ativas de seus ingredientes isoladamente: Panax pseudo ginseng - Notoginsenoside R1; Eucommia ulmoides -(±) Pinoresinol; Licorice root - Ácido Glicirrizínico. Os compostos não apresentaram efeitos na entrada, replicação e liberação de novas partículas virais. Devido à ausência de resultados bem delineados e tendo em vista os resultados das terapias anti-VHC atuais e futuras, é improvável que compostos naturais sejam utilizados ou chegarão ao desenvolvimento clínico nesta indicação / Worldwide is estimated that nearly 170 million people are infected with hepatitis C virus (HCV), highly correlated with the occurrence of chronic hepatitis and hepatocellular carcinoma. Hepatitis C patients present higher prevalence of steatosis when compared with the general population, ranging between 40% and 75%. There are two forms of steatosis in HCV infected patients: metabolic steatosis (risk factors) and cytopathic associated with genotype 3. Lipids are essential for the HCV replication cycle. It acts on different functions: as prosthetic groups into viral proteins and / or cellular cofactors in the HCV replication, as specific HCV components or as a constituent of lipovirals particles. Our group previously reported that the administration of the natural compound Yo Jyo Hen Shi Ko (YHK) inhibits steatosis development, decreases markers of oxidative stress and inflammation, improves aminotransferases concentration and decreases the visceral fat. Standard therapy for hepatitis C is a combination of pegylated interferon alpha (PEG-IFN-alfa), stimulating the host immune system to fight infection and the antiviral compound named ribavirin. Nowadays, Telaprevir, Boceprevir, Sofosbovir and Simeprevir are approved as new anti-HCV drugs; they act as protease inhibitors. Its efficiency, however, varies between genotypes, and the constant mutations of the virus can lead to resistance. The lack of vaccines, or a definitive therapy, stimulates the research of new compounds and alternative treatments. In this study, we evaluated the effect of YHK in HCV replication cycle due to the effect of YHK and the importance of lipid metabolism for HCV. For this purpose we used cell culture techniques allowing the study of different stages of HCV replication cycle: entry (HCVpp), replication - replicons JFH1 NS3-5B and Con1, also replication and infection-JC1-Fluc. We also used active compounds of its ingredients: Panax pseudo ginseng - Notoginsenoside R1; eucommia - (±) pinoresinol, Licorice root - Glycyrrhizinic Acid in order to elucidate a possible effect of a single component of the YHK formula in HCV. We could not observe any difference in HCV entry, replication and release in the presence of the four compounds. It is unlikely that natural compounds will be used or come to clinical development in this indication, due to the absence of well defined results and in view of the results of new anti-HCV therapies

Das Humane Cytomegalievirus (HCMV) ist ein ubiquitäres Pathogen, welches den Metabolismus der Wirtszelle auf vielfältige Weise manipuliert, um seine eigene Vermehrung zu begünstigen. In der vorliegenden Arbeit konnte nachgewiesen werden, dass auch das Ubiquitin-Proteasom-System in die HCMV-Replikation involviert ist. So konnte zunächst gezeigt werden, dass die Chymotrypsin-ähnliche (CT-L) Aktivität des konstitutiven Proteasoms in HCMV-infizierten Zellen signifikant erhöht ist. Wurde die CT-L Proteasomaktivität durch Proteasominhibitoren (PI) blockiert, so hatte dies die Hemmung der HCMV-Replikation zur Folge. Die Charakterisierung des Einflusses von PI auf die virale Proteinexpression ergab, dass bei niedriger MOI (MOI 0.1) deutlich verringerte Mengen der sehr frühen Proteine vorlagen, dieser Effekt jedoch bei hoher MOI (ab MOI 1) aufgehoben war. Die Expression früher Proteine war MOI-unabhängig reduziert. Hingegen war die Expression der späten Proteine MOI-unabhängig vollständig unterdrückt. Studien mit dem Nukleosidanalogon BrdU ergaben zudem, dass die de novo Synthese viraler DNA blockiert war. Um erste Hinweise auf den Wirkungsmechanismus von PI zu erhalten, wurde untersucht, ob der Transkriptionsfaktor NF-kappaB oder zelluläre Transkriptionsrepressoren wie z.B. hDaxx am anti-HCMV-Effekt beteiligt sind. Durch die Charakterisierung einer Virusmutante mit Deletion der NF-kappaB-Bindestellen im MIE-Enhancer/Promotor konnte gezeigt werden, dass der antivirale Effekt von PI nicht auf der Hemmung der Aktivierung von NF-kappaB beruht. Experimente mit hDaxx-knockdown Zellen ergaben hingegen, dass die Stabilisierung des Transkriptionsrepressors hDaxx partiell zum anti-HCMV-Effekt von PI beiträgt. Darüber hinaus müssen jedoch weitere virale oder zelluläre Zielproteine existieren, deren Beeinflussung durch PI kritisch für die Virusreplikation ist. Zusammenfassend stellt das Proteasom somit einen neu identifizierten potentiellen Angriffspunkt für die anti-HCMV-Therapie dar. / The Human Cytomegalovirus (HCMV) is a ubiquitous pathogen that manipulates many aspects of the host cell metabolism to enhance viral replication. This work demonstrates that the ubiquitin-proteasome system is also involved in HCMV replication. First of all, the chymotrypsin-like (CT-L) activity of the constitutive proteasome was significantly increased in HCMV infected cells. In the presence of proteasome inhibitors (PI) viral replication was efficiently blocked. Characterisation of the influence of PI on viral protein expression showed that immediate early protein expression was clearly reduced at low MOI (MOI 0.1); however, this effect was abolished at high MOI (starting from MOI 1). Expression of early proteins was significantly decreased independently of the MOI used for infection. In contrast, late protein expression was completely suppressed at both low and high MOI. Additionally, studies using the nucleoside analogue BrdU showed that PI block the de novo synthesis of viral DNA. In order to gain insight into the working mechanism of PI the involvement of the transcription factor NF-kappaB and cellular repressors of transcription (e.g. hDaxx) in the antiviral effect of PI was examined. Studies using a mutant virus carrying deletions of the NF-kappaB binding sites in the MIE-enhancer/promoter revealed that the anti-HCMV effect of PI is not due to inhibition of NF-kappaB activation. Analyses using hDaxx-knockdown cells showed that stabilisation of the transcriptional repressor hDaxx partially contributes to the antiviral effect of PI. However, the existence of additional viral or cellular target proteins of PI is very likely. In summary, the proteasome thus represents a newly identified and promising target for anti-HCMV therapy.

Estima-se que 170 milhões de pessoas no mundo estejam infectadas com o vírus da hepatite C (VHC), o que está altamente relacionado à ocorrência de hepatite crônica e carcinoma hepatocelular. A prevalência de esteatose hepática em doentes com hepatite C crônica é muito maior do que na população geral variando entre 40 a 75%. A associação entre a infecção pelo VHC e esteatose hepática é multifatorial. Duas formas de esteatose hepática são encontradas em pacientes com hepatite C crônica: esteatose metabólica (fatores de risco) e citopática relacionada ao genótipo 3a. Os lipídios são essenciais para o ciclo de replicação do VHC, eles podem exercer seu efeito em diferentes níveis como: grupos prostéticos em proteínas virais e/ou cofatores celulares na replicação de VHC, componentes especializados na estrutura do VHC onde ocorre a replicação ou como constituinte das partículas lipovirais. Trabalhos experimentais realizados anteriormente por nosso grupo relataram que a administração do composto natural Yo Jyo Hen Shi Ko (YHK) promove a inibição do desenvolvimento da esteatose, redução dos marcadores de estresse oxidativo, menor escore de inflamação, melhora nas concentrações de aminotransferases e diminuição da gordura visceral em um modelo animal de esteato-hepatite não alcoólica. A terapia padrão da hepatite C consiste em uma combinação de interferon peguilado alfa (PEG-IFN-alfa) que estimula o sistema imunológico do hospedeiro para combater a infecção e o composto antiviral ribavirina. Atualmente foram aprovados pelas agências de saúde os inibidores de protease Boceprevir, Telaprevir, Daclatasvir e Simeprevir. No entanto, sua eficiência varia entre os genótipos e as constantes mutações do vírus podem levar a resistência. A falta de uma vacina ou uma terapia definitiva faz com que diversos compostos com diferentes mecanismos de ação sejam testados como possíveis alternativas de tratamento. Tendo em vista a capacidade do YHK de reduzir a esteatose e a importância do metabolismo para a replicação do VHC, o objetivo deste trabalho foi avaliar o efeito do YHK no ciclo celular do VHC. Para isso foram utilizadas técnicas de cultura celular que permitem o estudo das diferenças fases do ciclo de replicação do VHC: entrada (VHCpp), replicação - replicons JFH1-NS3-5B e Con1, replicação e infecção- JC1-Fluc. De forma a elucidar a possibilidade de um único componente da fórmula YHK apresentar efeito sobre o VHC, foram utilizadas para comparação as substâncias ativas de seus ingredientes isoladamente: Panax pseudo ginseng - Notoginsenoside R1; Eucommia ulmoides -(±) Pinoresinol; Licorice root - Ácido Glicirrizínico. Os compostos não apresentaram efeitos na entrada, replicação e liberação de novas partículas virais. Devido à ausência de resultados bem delineados e tendo em vista os resultados das terapias anti-VHC atuais e futuras, é improvável que compostos naturais sejam utilizados ou chegarão ao desenvolvimento clínico nesta indicação / Worldwide is estimated that nearly 170 million people are infected with hepatitis C virus (HCV), highly correlated with the occurrence of chronic hepatitis and hepatocellular carcinoma. Hepatitis C patients present higher prevalence of steatosis when compared with the general population, ranging between 40% and 75%. There are two forms of steatosis in HCV infected patients: metabolic steatosis (risk factors) and cytopathic associated with genotype 3. Lipids are essential for the HCV replication cycle. It acts on different functions: as prosthetic groups into viral proteins and / or cellular cofactors in the HCV replication, as specific HCV components or as a constituent of lipovirals particles. Our group previously reported that the administration of the natural compound Yo Jyo Hen Shi Ko (YHK) inhibits steatosis development, decreases markers of oxidative stress and inflammation, improves aminotransferases concentration and decreases the visceral fat. Standard therapy for hepatitis C is a combination of pegylated interferon alpha (PEG-IFN-alfa), stimulating the host immune system to fight infection and the antiviral compound named ribavirin. Nowadays, Telaprevir, Boceprevir, Sofosbovir and Simeprevir are approved as new anti-HCV drugs; they act as protease inhibitors. Its efficiency, however, varies between genotypes, and the constant mutations of the virus can lead to resistance. The lack of vaccines, or a definitive therapy, stimulates the research of new compounds and alternative treatments. In this study, we evaluated the effect of YHK in HCV replication cycle due to the effect of YHK and the importance of lipid metabolism for HCV. For this purpose we used cell culture techniques allowing the study of different stages of HCV replication cycle: entry (HCVpp), replication - replicons JFH1 NS3-5B and Con1, also replication and infection-JC1-Fluc. We also used active compounds of its ingredients: Panax pseudo ginseng - Notoginsenoside R1; eucommia - (±) pinoresinol, Licorice root - Glycyrrhizinic Acid in order to elucidate a possible effect of a single component of the YHK formula in HCV. We could not observe any difference in HCV entry, replication and release in the presence of the four compounds. It is unlikely that natural compounds will be used or come to clinical development in this indication, due to the absence of well defined results and in view of the results of new anti-HCV therapies

L’infection par le cytomégalovirus est le plus souvent asymptomatique chez les sujets immunocompétents mais entraine une morbidité et une mortalité importantes chez les patients immunocompromis et en cas d’infection congénitale.<p>Après l’infection primaire, le virus persiste tout au long de la vie à l’état latent mais peut se réactiver de manière intermittente. Ceci est associé à l’expansion de lymphocytes T CD4+ fortement différenciés ayant des fonctions auxiliaires et cytolytiques. L’infection primaire est, par contre, caractérisée par une réplication virale intense qui dure plusieurs mois. Il a été montré que l’exposition prolongée à des concentrations élevées d’antigènes entraine une perte progressive de fonction par les lymphocytes T appelée épuisement et caractérisée par l’expression de récepteurs inhibiteurs. L’impact de la réplication virale intense observée au cours de l’infection primaire par le CMV sur la fonction des lymphocytes T CD4+ n’est pas bien connu.<p>La fonctionnalité des lymphocytes T CD4+ a été explorée chez l’humain et le singe rhésus au cours de l’infection primaire et comparée à celle de sujets porteurs chroniques du virus.<p>Les résultats montrent que l’infection primaire par le CMV est associée à la détection de lymphocytes T CD4+ circulants ayant une faible capacité de prolifération et de production de cytokines et d’IL-2 en particulier.<p>L’impact de la différenciation sur la fonction des lymphocytes a été exploré en détail chez l’humain. Il a été observé qu’un degré de différenciation plus élevé des lymphocytes T CD4+ spécifiques du CMV joue un rôle dans la production réduite d’IL-2. Toutefois, la fraction moins différenciée (exprimant la molécule CD28) présente également une sécrétion d’IL-2 moindre au cours de l’infection primaire. Ceci fait partie d’une diminution globale de la production de cytokines au cours de l’infection primaire qui affecte également la sécrétion d’IFNγ et TNFα, entraine une polyfonctionnalité réduite et est indépendante de la différenciation. L’épuisement des lymphocytes T CD4+ spécifiques du CMV contribue à leur fonctionnalité moindre comme l’indique l’expression accrue du récepteur inhibiteur PD-1 et l’augmentation des réponses prolifératives en présence d’anticorps bloquant PD-1.<p>Le lien entre excrétion virale et fonction lymphocytaire a été étudié chez le macaque rhésus. L’infection par le CMV est observée chez les singes juvéniles et adultes mais pas chez les nourrissons. L’excrétion urinaire et salivaire est significativement plus fréquente et intense chez les singes juvéniles par rapport aux adultes. Comme chez l’humain au cours de l’infection primaire, les lymphocytes T CD4+ spécifiques du virus sont moins<p>polyfonctionnels et prolifèrent moins efficacement chez les singes juvéniles par rapport aux singes adultes. Ceci est associé à l’expression accrue du récepteur inhibiteur PD-1 chez les singes juvéniles. La réponse proliférative des lymphocytes T CD4+ est accrue en présence d’anticorps bloquant PD-1 ou d’IL-2 exogène. Enfin, une association inverse entre fonction lymphocytaire et excrétion urinaire a été mise en évidence chez les macaques adultes.<p>Ces résultats indiquent que l’infection par le CMV présente des caractéristiques semblables chez l’humain et le singe rhésus. L’infection primaire est associée à la détection de lymphocytes T CD4+ ayant une fonctionnalité moindre qu’au cours de l’infection chronique. L’expression du récepteur inhibiteur PD-1 typique des cellules épuisées est l’un des mécanismes impliqués et pourrait être la cible de stratégies immunomodulatrices visant à améliorer les fonctions lymphocytaires et le contrôle de la réplication virale. Les résultats présentés indiquent que l’infection naturelle chez le singe rhésus constitue un modèle potentiellement utile à l’étude de la réponse immune au CMV humain et à l’évaluation de stratégies immunomodulatrices.<p>/<p>Cytomegalovirus infection is mostly asymptomatic in immunocompetent hosts but leads to severe morbidity and mortality in immunocompromised subjects and foetuses.<p>After primary infection, CMV establishes lifelong persistence but can reactivate intermittently. This is associated with the expansion of highly differentiated CD4+ T lymphocytes exhibiting helper functions and cytolytic activity.<p>Primary infection is characterised by an intense viral replication lasting several months. It has been shown that prolonged exposure to elevated antigen concentrations induces a progressive loss of function by T lymphocytes called exhaustion. This state of functional impairment is associated to the expression of inhibitory receptors. The consequence of the intense viral replication seen in primary CMV infection on CD4+ T cell function is unknown.<p>CD4+ T cell function has been studied in human and rhesus macaque during primary CMV infection. Chronic CMV carriers have been used as controls.<p>The results show that primary CMV infection is associated to the detection of circulating CD4+ T lymphocytes exhibiting weak proliferative capacities and reduced cytokine production affecting IL-2 in particular.<p>The impact of differentiation on lymphocyte function has been explored in detail in human. An increased proportion of terminally differentiated CD4+ T cells (CD28-) is observed during primary infection. These lymphocytes are unable to secrete IL-2 in response to CMV antigens. Interestingly, CD28+ CMV-specific CD4+ T cells also exhibit reduced IL-2 production during primary infection. This is part of a global reduction of cytokine production affecting IFNγ and TNFα as well. The impaired cytokine production is associated to reduced polyfunctionality and is independent of differentiation. Exhaustion of CMV-specific CD4+ T lymphocytes contributes to the reduced functionality as shown by an increased expression of the inhibitory receptor PD-1 and improved proliferative responses in the presence of PD-1 blocking antibodies.<p>The relationship between viral replication and lymphocyte function has been explored in rhesus macaques. CMV infection is observed in juvenile and adult monkeys but not in newborns. Excretion in urine and saliva is significantly more frequent and intense in juvenile monkeys than adults. As in primary infection in human, CMV-specific CD4+ T lymphocytes are less polyfunctional and have lower proliferative capacities in juveniles as compared to adults. This is associated with an increased expression of PD-1 in juvenile monkeys. CD4+ T cell proliferative responses are increased when PD-1 blocking antibodies or exogenous IL-2 are added to the culture medium. Finally, an inverse association between lymphocyte function and urinary excretion has been observed in adult macaques.<p>These results indicate that CMV infection shares common features in human and rhesus macaque. Primary infection is associated to the detection of CD4+ T lymphocyte displaying lower functional capacities as compared to chronic infection. Exhaustion contributes to the functional impairment and the inhibitory receptor PD-1 could be targeted by immunomodulatory strategies aiming at improving lymphocyte functions and controlling viral replication. Natural CMV infection in rhesus macaque might be useful as a model to evaluate the efficacy and safety of immunomodulatory approaches. / Doctorat en Sciences médicales / info:eu-repo/semantics/nonPublished

Morbilliviruses belong to the family Paramyxoviridae of the Mononegavirale order of viruses. The Mononegavirale order contains viruses which contain negatively-polar, non-segmented and single stranded RNA genomes. This order contains some of most lethal pathogens known to the humankind. Ebola virus and Marburg virus are perhaps the most lethal human pathogens. Rinderpest virus, declared eradicated in 2011, was known to be the most significant cattle killer. Similarly the Canine distemper virus and Rabies virus, two topmost canine pathogens belong to this order. The L protein in the viruses of Morbillivirus genus harbours the viral RNA-dependent RNA polymerase that replicates and transcribes the viral genome and also all the mRNA capping enzymes, viz. RNA 5’ triphosphatase, guanylyltransferase, RNA (guanine-7-)methyltransferase and RNA 5’ cap-dependent (2’-oxo-)methyltransferase. Moreover this protein can act as a protein kinase that can regulate the function of P protein which serves as a switch between transcription and replication. mRNA capping is necessary for the virus for the purpose of exploiting host cellular machinery towards viral protein synthesis. The Rinderpest virus L protein serves as a model to study the capping enzymes of Morbillivirus. RNA triphosphatase (RTPase), the first enzyme of the capping cascade had earlier been located on the L protein. The RTPase minimal domain on the L protein was identified earlier by sequence homology studies done with RTPase proteins of Baculovirus and Vaccinia virus and cloned. The bacterially expressed recombinant domain was shown to possess RTPase activity. The enzymatic activity was characterized and the RTPase was found to be a metal-dependent enzyme which is highly specific to capping viral mRNA. Further characterization of the domain revealed that the domain also possesses nucleotide triphosphatase (NTPase), tripolyphosphatase and pyrophosphatase activities. Two site-directed mutants in motif-A of the domain: E1645A and E1647A were also tested and were found to be essential for the RTPase and NTPase activity. It was also recognized through these mutant studies that the active sites of RTPase and NTPase activities are partially overlapping. Earlier work done with Vesicular stomatitis virus capping enzymes showed that the Rhabdoviridae family of viruses follow unconventional capping pathway utilizing an enzyme polyribonucleotidyltransferase (PRNTase) which transfers GDP to 5’-monophosphated RNA. Characterization of the RTPase activity which converts 5’-triphosphated RNA into 5’-diphosphated RNA is an evidence for the morbilliviruses utilizing the conventional eukaryotic capping cascade. The results show that Paramyxoviridae do not follow unconventional capping pathway for the mRNA capping as has been the paradigm in the past decade.

Introduction: le Virus Respiratoire Syncytial humain (RSV) induit un taux élevé de morbidité et de mortalité chez les enfants, les personnes immunodéprimées et les personnes âgées. Il existe un besoin urgent d'un nouveau traitement antiviral et d'un vaccin efficaces. Les cellules épithéliales des voies aériennes (AEC) sont la cible principale de RSV et constituent la première ligne de défense grâce à des mécanismes distincts, qui incluent une réponse antivirale autonome cellulaire. La protéine p62/SQSTM1 a de multiples fonctions cellulaires, y compris la séquestration spécifique de la cargaison ubiquitinée (c'est-à-dire, les protéines/organelles et les bactéries intracellulaires) pour leur clairance par autophagie. Des données publiées ont mis en évidence un rôle important de p62 dans la régulation de plusieurs virus (par exemple, le virus de la grippe et la dengue), favorisant ou restreignant sa réplication en fonction du virus. L'objectif de notre étude est de déterminer le rôle de p62 dans la régulation du cycle infectieux de RSV. Méthodes et résultats: L'analyse de l'expression de p62 dans les cellules A549 a montré que p62 est induit et phosphorylé au début de l'infection par RSV. Il est ensuite dégradé plus tardivement durant l’infection. La déplétion des niveaux de p62 a diminué l'accumulation intracellulaire des protéines virales, tandis que la relâche des virions infectieux a été augmentée. De plus, nous avons observé que la réplication de recRSV-GFP est diminuée dans des cellules exprimant de façon stable la protéine associée aux microtubules 1A/1B, chaîne légère 3 (LC3). LC3 recrute p62 et ses cargaisons à l'autophagosome pour qu'ils soient dégradés par autophagie. Des études sont actuellement en cours pour déterminer les mécanismes moléculaires, dépendant de p62, impliqués dans la régulation de la réplication de RSV. Conclusion: nos résultats mettent en évidence un rôle clé de p62 dans la réplication et la propagation de RSV. Ces études aideront à définir si p62 pourrait représenter une cible thérapeutique potentielle pour lutter contre l'infection à RSV. / Introduction: Human respiratory syncytial virus (RSV) causes a high rate of morbidity and mortality worldwide in children, immunocompromised and elderly people. There is an urgent need for effective antiviral treatments and vaccines for RSV. Airway epithelial cells (AECs) are the primary target of RSV and constitute the first line of defense through distinct mechanisms, including intrinsic antiviral responses. The p62/SQSTM1 protein has multiple cellular functions including cell signaling and sequestration of specific ubiquitinated cargo (i.e. proteins/organelles and intracellular bacteria) for autophagic degradation. The replication of several viruses has been shown to be sensitive to p62 levels. The goal of our study is to investigate the role of p62 in the regulation of RSV replication. Methods and Results: Analysis of p62 expression in A549 cells showed that p62 is induced and phosphorylated during early stages of RSV infection, followed by degradation at later times. P62 silencing diminished the intracellular accumulation of viral proteins, while causing increased release of infectious virions. Additionally, we observed that the stable expression of Microtubule-associated protein 1A/1B-light chain 3 (LC3), which recruits p62 and its cargos to the autophagosome for autophagy degradation, reduces recRSV-GFP replication. Studies are currently undertaken to determine the molecular mechanisms involved in p62-dependent regulation of RSV replication. Conclusion: Our results highlight a key role of p62 in the replication of RSV. These studies will help to define whether p62 might represent a potential therapeutic target to fight RSV infection.

Rotavirus is one of the leading etiological agents of gastroenteritis in young of many species including humans worldwide and is responsible for about 600,000 infant deaths per annum. Rotavirus belongs to the Reoviridae family, and its genome is composed of 11 double-stranded RNA segments that encode six structural proteins and six nonstructural proteins. Rotavirus replication is fully cytoplasmic and occurs within highly specialized regions called viroplasms. NSP2 and NSP5 have been shown to be essential for viroplasm formation and, when co-expressed in uninfected cells, to form viroplasm¬like structures. A recent study suggest a key role for NSP5 in architectural assembly of viroplasms and in recruitment of viroplasmic proteins, containing four structural (VP1, VP2, VP3 and VP6) and two nonstructural (NSP2 and NSP5) proteins. NSP5, the translation product of gene segment 11 has a predicted molecular eight of 21 kDa. NSP5 has been reported to exist in multiple isoforms ranging in size from 28-and 32-35 kDa from a 26-kDa precursor has been attributed to O-glycosylation and hyperphosphorylation. To study different properties of the protein, recombinant NSP5 containing an N-terminal hisidine tag was expressed in bacteria and purified by affinity chromatography. A significant observation was the similarity in phosphorylation property of the bacterially expressed and that expressed in mammalian cells. While the untagged recombinant protein failed to undergo phosphorylation in vitro, addition of His tag or deletions at the N-terminus promoted phosphorylation of the protein in vitro, which is very similar to the reported properties exhibited by the corresponding proteins expressed in mammalian cells. Phosphorylation of NSP5 in vitro is independent of the cell type from which the extract is derived suggesting that the kinases that phosphorylate NSP5 are distributed in all cell types. Among the C-terminal deletion mutants studied, NH-∆C5 and NH-∆C10 were phosphorylated better than full-length NSP5, but NH-∆C25 and NH¬∆C35 showed substantial reduction in the level of phosphorylation compared to full-length NSP5. These results indicate that the C-terminal 30 residues spanning the predicted α-helical domain of NSP5 are critical for its phosphorylation in vitro which is in correspondence with previous findings that C-terminal 21 amino acids of NSP5 direct its insolubility, hyperphosphorylation, and VLS formation. The results revealed that though the tagged full-length and some of the mutants could be phosphorylated in vitro, they are not suitable substrates for hyperphosphorylation unlike the similar proteins expressed in mammalian cells or infected cells. Analysis by western blot and mass spectrometry revealed that the bacterially expressed NH-NSP5 is indeed phosphorylated. It appears that prior phosphorylation in bacteria renders the protein conformationally not amendable for hyperphosphorylation by cellular kinases in vitro. Mutation of the highly conserved proline marginally enhanced its phosphorylation in vitro but the stability of protein is affected. Notably, mutation of S67A, identified as a critical residue for the putative caesin kinase-I and-II pathways of NSP5 phosphorylation, affected neither the phosphorylation nor the ATPase activity of NSP5. These results suggest that bacterially expressed NSP5 by itself has undectable auto-kinase activity and it is hypophosphorylated. Purified recombinant NSP5 has been reported to possess an Mg¬ 2+-dependent ATP-specific triphosphatase activity. The results indicated that deletion of either C-terminal 48 amino acids or N-terminal 33 residues severely affected the ATPase activity of recombinant NSP5, underlying the importance of both N-and C-terminal domains for NSP5 ATP hydrolysis function. NSP5 expressed in rotavirus infected cells exists as inter-molecular disulfide-linked dimeric forms and it appears that the 46 kDa isoforms, that are phosphorylated, corresponds to dimer as revealed by western blotting. Analytical gel filtration analysis of NH-NSP5, NH-ΔN43 and NH-ΔN33-ΔC25 showed most of the proteins in void volume, but an additional peak corresponding to the mass of dimeric species further supports that NSP5 is basically a dimer that undergoes oligomerization. Analysis by sucrose-gradient fractionation revealed that NH-NSP5 and NH-ΔN43 proteins were mainly distributed in the lower fraction of the gradient suggesting the existence of high molecular weight complexes or higher oligomers. The multimeric nature of NSP5 and its mutants was further confirmed by dynamic light scattering which suggests that high molecular weight complexes are of homogenous species. The correlation curves showed a low polydispersity distribution and a globular nature of recombinant NH-NSP5 proteins. The present results clearly demonstrate that dimer is the basic structural unit of NSP5 which undergoes oligomerization to form a complex consisting of about 20-21 dimers. The nonstructural protein 5 is hyperphosphorylated in infected cells and cellular kinases have been implicated to be involved in its phosphorylation. NSP5 contains multiple consensus sites for phosphorylation by several kinases, but the cellular kinases that specifically phosphorylate NSP5 in infected cells are yet to be identified. Previous studies from our laboratory using signaling pathway inhibitors revealed that recombinant NH¬NSP5 and its deletion mutants can be phosphorylated in vitro by purified cellular kinases and by mammalian cell extracts. These studies also showed the involvement of PI3K-Akt and MAPK signaling pathways in NSP5 phosphorylation and a negative role for GSK3β in the phosphorylation of bacterially expressed recombinant NSP5 in vitro. In the present work, using phospho-specific anti-Ser9 GSK3β antibody, we observed that GSK3β is inactivated in a rotavirus infected MA104 cells in a strain-independent manner. GSK3β¬specific small interfering RNA (siRNA-GSK3β) reduced GSK3β levels leading to increased level of synthesis of the structural rotavirus protein VP6 and NSP5 hyperphosphorylation compared to control siRNA. The pharmacological kinase inhibitors (LY294002, Genistein, PD98059, and Rapamycin) studies at the concentrations tested did not significantly affect rotavirus infection as seen from the number foci, while U0126 severely affected rotavirus replication. The results clearly demonstrated the importance of the MEK1/2 signaling pathway in the successful replication of rotavirus and NSP5 hyperphosphorylation in rotavirus-infected cells. In contrast inhibition of GSK3β activity by LiCl, increased in general, the number of foci by greater than 2-fold for all viral strains studied. These results suggest that MEK1/2 pathway majorly contributes to GSK3β inactivation in rotavirus infected cells. Thus, our results reveal that rotavirus activates both the PI3K/Akt and FAK/ERK1/2 MAPK pathways and appears to utilize them as a strategy to activate mTOR, and inhibit GSK3β through phosphorylation on serine 9, the negative regulator of rotavirus NSP5 phosphorylation, and thus facilitate translational competence of rotaviral mRNAs during virus replication cycle. It was shown previously in the laboratory by co-immunoprecipitation assay that Hsp70 interacts with rotaviral proteins VP1 and VP4 in rotavirus-infected mammalian cells. In this study, the interactions between Hsp70 with VP1 and VP4 were further evaluated in vitro by GST-pull down assay. It was observed that the N-terminal ATPase and C-terminal peptide-binding domain of Hsp70 is necessary for its direct interaction with VP1 and VP4. The presence of Hsp70 in purified double-and triple-layered virus particles further supported the observed interactions of rotaviral proteins VP1 and VP4 with Hsp70. However, the specific interaction observed between Hsp70 and rotaviral capsid proteins, VP1 and VP4 in viral particles suggests that Hsp70 has an important role during rotavirus assembly which requires further investigation.