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<p>Coronaviruses are the largest known RNA viruses and infect a wide range of hosts. Human coronaviruses traditionally have been known to be the cause of the common cold and have been vastly understudied due to low morbidity and mortality. The emergence of SARS-CoV and MERS-CoV has altered the landscape of coronavirus research and proven the deadly capabilities of human coronaviruses. With two recent zoonotic events, it is increasingly important to understand the molecular biology of human coronaviruses. The coronavirus nucleocapsid protein is an essential structural protein that complexes with the viral genome. Though nucleocapsid formation is the protein’s major role, it has also been found to have other functions and effects during infection. The following research aimed to examine how the human coronavirus nucleocapsid protein affects the innate immune response <em>in vitro</em>. Modulation of the type I interferon response by the nucleocapsid was first investigated and the nucleocapsids were shown to have the ability to block interferon signalling. Additionally, the nucleocapsid protein was found to cause a dysregulation of transcription factor NFKB1. We propose a novel mechanism of this NFKB1 negative regulation interference. Taken together, we have further characterized the significant role of the coronavirus nucleocapsid protein in innate immune evasion.</p> / Doctor of Philosophy (Medical Science)

In organisms from insects to vertebrates, Toll-like receptors (TLRs) are primary pathogen detectors that activate downstream pathways, specifically those that direct expression of innate immune effector genes. TLRs also have roles in development in many species. The sea anemone Nematostella vectensis is a useful cnidarian model to study the origins of TLR signaling because its genome encodes a single TLR and homologs of many downstream signaling components, including the NF-κB pathway. In this dissertation, the single N. vectensis TLR (Nv-TLR) is characterized. It is demonstrated that Nv-TLR can activate canonical NF-κB signaling in human cells, the intracellular TIR domain of Nv-TLR can interact with human TLR adapter proteins MAL and MYD88, and the TIR domain of Nv-TLR is required for NF-κB activation. It is shown that the coral pathogen Vibrio coralliilyticus causes a rapidly lethal disease in N. vectensis and that heat-inactivated V. coralliilyticus and bacterial flagellin can activate a reconstituted Nv-TLR-to-NF-κB pathway in human cells. By immunostaining of anemones, Nv-TLR is shown to be expressed in a subset of cnidocytes and many of these Nv-TLR-positive cells also express Nv-NF-κB. Additionally, the nematosome, which is a Nematostella-specific multicellular structure, expresses Nv-TLR, many innate immune pathway homologs, and can engulf V. coralliilyticus. Morpholino knockdown indicates that Nv-TLR also has an essential role during early embryonic development. The characterization of this primitive TLR and identification of a bacterial pathogen for N. vectensis reveal ancient TLR functions and provide a novel model for studying the molecular basis of cnidarian disease and immunity.

Legionella pneumophila ist der Erreger der Legionärskrankheit. Die Pathogenität des Bakteriums basiert auf seiner Fähigkeit innerhalb menschlicher Lungenzellen zu überleben und sich zu vermehren. Demzufolge ist L. pneumophila nicht nur interessant als wichtiges Pathogen, sondern kann auch als Sonde verwendet werden, um allgemeine intrazelluläre Ereignisse zu untersuchen. Ein Beispiel hierfür ist die, durch das Pathogen gestörte, intrazelluläre Kommunikation zwischen den Organellen des endoplasmatischen Retikulums (ER) und dem Golgi Apparat (GA). In der vorliegenden Studie schlagen wir ein neues Modell vor, wie das Bakterium erfolgreich seine replikative Nische, die Legionella Vakuole (LV), innerhalb des Zytosols aufbauen könnte, um seine Ausbreitung zu garantieren. Um die Mechanismen für die erfolgreiche Ausbeutung der Wirtszelle gezielt untersuchen zu können, haben wir mit Hilfe von siRNA spezifisch verschiedene Wirtszellproteinen herunterreguliert und den Einfuß der Abwesenheit dieser Proteine auf die Vermehrung von L. pneumophila gemessen. Die Ergebnisse wiesen darauf hin, dass die LV möglicherweise den Golgi Apparat imitiert und auf diese Weise den zellulären Vesikeltransport umleitet. Diese Theorie wurde durch in silico Ergebnisse unterstützt, die in der Proteinsequenz des Legionella Effektor-Proteins LidA, das auf der Vakuole lokalisiert ist, ein SNARE-ähnliches Motiv zeigte. Dies weist auf ein auf der Vakuole lokalisiertes SNARE-Erkennungsmotiv hin, das notwendig sein könnte, um zelluläre Transportvesikel zu koppeln. Aus dem Wissen heraus, dass L. pneumophila in der Lage ist, die Aktivierung der zellulären Proteine Arf1 und Rab1 durch Phosphorylierung und Dephosphorylierung zu regulieren, machten wir uns auf die Suche nach Proteinen, die auf Infektion hin modifiziert werden. Die Kommunikation von Wirt und Pathogen über Phosphorylierung ist bekannt im Bezug auf pathogenspezifische Modifikation des Zytoskeletts und Signalkaskaden in der Anti-Apoptose. Für diese Studie wurde ein Antikörper verwendet, der spezifisch phosphorylierte Tyrosinreste erkennt. Dies resultierte in der Detektion einer Serin-Threonin-Kinase in der Amöbe Acanthamöba castellanii, die an einem Tyrosinrest phosphoryliert ist. Diese Amöben-Kinase wies in silico Homologie zu der humanen GS-Kinase 3 des Wnt-Signalwegs, bekannt aus der Forschung der embronalen Entwicklung bei Drosophila, auf. Der letzte Teil dieser Arbeit konzentrierte sich auf die, durch eine L. pneumophila-Infektion ausgelöste, anti-apoptotische Signalkaskade. Es ist bekannt, dass auf eine Infektion hin NF-kappaB aktiviert wird. Dies führt dazu, dass p65 in den Zellkern wandert und dort als Transkriptionsfaktor aktiv wird. Diese Translokation geschieht in 2 zeitversetzten Phasen. Eine Aktivierungsspitze wird nach dem Kontakt mir bakteriellem Flagellin gemessen, gefolgt, von einer dauerhaften Aktivierung, abhängig von einem funktionierenden Dot/ Icm Typ-IV-Translokationssystem. In dieser Arbeit stießen wir auf eine L. pneumophila Mutante, die den Dot/ Icm-Effektor SdbA nicht bildet, und die daraufhin NF-appaB nicht aktivieren kann. Diese Mutante war ebenfalls nicht in der Lage, sich in Epithelzellen zu vermehren. Dies ist außergewöhnlich, da das L. pneumophila Effektor Repertoire so redundant ist, dass die Abwesenheit eines einzigen Effektors selten einen so starken Einfluss auf die Replikation hat. All diese Ergebnisse zeigen zusammengenommen, auf wie vielen verschiedenen Ebenen L. pneumophila in der Lage ist, seine Wirtszelle zu manipulieren, um einerseits die nötige Nische für seine Vermehrung zu etablieren und andererseits die Zelle am Selbstmord zu hindern. Dies geschieht durch Imitation zellulärer Prozesse. / Legionella pneumophila is the causative agent of Legionnaires´ disease. The bacterium’s pathogenicity is based on its ability to survive and multiply efficiently inside human alveolar cells. Therefore, L. pneumophila is not only an important pathogen, but can also be used as a probe to investigate host cell function as for example, in the cellular trafficking pathway. In this study, we establish a new model of how this pathogen efficiently constructs its replicative niche, the Legionella containing vacuole (LCV), inside the host cytosol, enabling its dissemination. To investigate the mechanisms that lead to effective exploitation of the host cell, we down-regulated specific host cellular proteins via siRNA technology and measured the subsequent impact on L. pneumophila replication. The results suggest that the LCV mimicks the Golgi apparatus and via this mechanism hijacks host cellular vesicular trafficking. The L. pneumophila secreted effector protein LidA, located within the LCV, is shown to have a SNARE-like motif, suggesting a SNARE like sole connected to the LCV. Since it is known that cellular signalling proteins are controlled via phosphorylation and dephosphorylation, we went on to search for specifically modulated host cell proteins after L. pneumophila infection. The cross-talk of the pathogen with its host via phosphorylation has been connected to several sub-cellular activities leading to, for instance, cytoskeleton rearrangement and signalling events including anti-apoptosis pathways. Here we used a phosphorylated tyrosine antibody resulting in the detection of an amoeba serine-threonine-kinase, phosphorylated at its tyrosine residue. This kinase shows homologies to the human GSK3 of the wnt-signalling pathway. (“Wnt“ is merged from the names of the homologues genes Wg (Drosophila melanogaster) and Int (mouse) both employed in evolutionary developement.) The final part of this work concentrated on anti-apoptotic signalling events induced upon L. pneumophila infection. It is known that during L. pneumophila infection the activation of NF-kappaB and subsequent translocation of p65 from the cytosol into the nucleus follows a biphasic pattern. One short peak of activation is induced upon contact with bacterial flagellin, succeeded by a permanent Dot/ Icm type IV secretion system-dependent activation. In this study, we found the L. pneumophila mutant lacking the Dot/ Icm effector SdbA to be unable to activate NF-kappaB. This mutant also showed impaired growth in epithelial cells. This is remarkable due to the high redundancy of the L. pneumophila effector system, meaning deletion of a single effector rarely has such a big impact on replication. Taken together this work demonstrates, the manifold ways in which L. pneumophila on the one hand side establishes its niche to ensure replication and on the other hand side to bars its host cell from suicide. All of this is managed by mimicking cellular processes.

La survie des êtres vivants repose sur leur capacité d'adaptation à leur environnement et au maintien de l'homéostasie cellulaire. Au cours de mon doctorat, je me suis intéressée à deux de ces aspects : d'abord à la réponse immunitaire innée et inflammatoire par l'étude des voies associées aux facteurs de transcription NF-kB et ensuite à l'autophagie, qui consiste en la capacité d'une cellule à dégrader certains composants cellulaires ou des pathogènes intracellulaires. La rapidité d'activation/inactivation de ces processus cellulaires est permise par des modifications post-traductionnelles de certains acteurs parmi lesquelles l'ubiquitination des protéines, qui consiste en la liaison covalente de mono- ou polymères d'ubiquitines sur des protéines, et qui apparaît désormais comme un mécanisme majeur. Dans ce contexte, mes travaux ont consisté d'une part, en la mise en évidence de la fonction de la déubiquitinase USP36 dans la régulation de la voie immunitaire NF-B associée au récepteur 1 au TNFa (TNF-R1) en cellules humaines en culture. J'ai montré par des approches de biologie cellulaire et de biochimie qu'USP36 est un régulateur négatif spécifique de cette voie et est constitutivement associée au récepteur, contribuant ainsi à la régulation de l'ubiquitination de RIP1, un composant essentiel de la voie du TNF-R1. De cette étude, nous avons conclu qu'USP36 est un acteur clé de la voie du TNF-R1 permettant la répression de la voie en absence d'activation et favorisant un retour à l'état stationnaire en réponse à une stimulation au TNFa. D'autre part, mes travaux ont consisté en la réalisation d'un crible génétique in vivo chez la Drosophile pour l'identification de déubiquitinases impliquées dans la régulation de l'autophagie. J'ai identifié UBPY et USP12 dont la perte de fonction affecte à la fois la progression de l'autophagie et de l'endocytose. A partir de l'étude de ces enzymes, nous avons pu établir qu'une voie endocytaire intacte est requise pour le bon fonctionnement de l'autophagie. / The survival of living organisms is based on their ability to adapt to their environment and to maintain their cellular integrity. During my PhD, I was interested in two of these aspects: first, the innate immunity and inflammatory response through the study of the NF-kB-associated pathways, and then in autophagy, consisting in the ability of a cell to degrade some cellular components or intracellular pathogens. The rapid activation/inactivation of these cellular processes is permitted by the post-translational modifications of some components. Among these changes, protein ubiquitination, consisting in the covalent binding of ubiquitin mono- or polymers on target proteins, appears to be an essential mechanism. In this context, my work consisted on one hand, in showing the function of the deubiquitinating enzyme USP36 in the regulation of the immune pathway depending on the TNFa-associated receptor 1 (TNF -R1) pathway in cultured human cells. Using cellular and biochemical approaches, I showed that USP36 is a specific negative regulator of this pathway, constitutively associated with the receptor and which contributes to the regulation of the ubiquitination status of RIP1, which plays a major role in signal transduction. From this study, we conclude that USP36 is a key component of the TNF-R1 pathway, allowing for the repression of this pathway without stimulation and promoting the return to the steady-state after TNFa; treatment. On the other hand, I performed a genetic screen in vivo in Drosophila for the identification of deubiquitinating enzymes involved in regulating autophagy. I identified UBPY and USP12, whose loss-of-function affects both progression of autophagy and endocytosis. Further investigations allowed us to establish that an intact endocytic pathway is required for productive autophagy.

A sepse envolve mecanismos complexos de respostas imunológicas e inflamatórias, e o papel do NF- B é essencial. A diminuição da NO sintase endotelial (eNOS) durante a sepse contribui com a disfunção endotelial. A eritropoietina (EPO) é uma citocina protetora de diversos tecidos durante o estresse. Investigamos o papel da EPO na injúria renal aguda (IRA) induzida pela sepse usando o modelo de ligadura e punção do ceco (LPC). Ratos Wistar foram divididos em três grupos: controle; LPC e LPC+EPO (EPO, 4.000UI/kg, administrada 24h e 1h antes da cirurgia). Com a finalidade de estudar os efeitos precoces e tardios da EPO sobre a IRA induzida pela sepse realizamos três etapas de experimentos: Primeira etapa: 24 horas após LPC; Segunda etapa: 48 horas após LPC; Terceira etapa: análise de sobrevida. No estudo precoce o grupo LPC+EPO apresentou clearance de inulina significativamente maior que o grupo LPC. Recuperou os níveis de hematócrito na sepse, melhorou a pressão arterial e a acidose metabólica. No estudo tardio o grupo LPC+EPO apresentou clearance de creatinina significativamente maior que o grupo LPC. Nesta fase tardia a EPO recuperou os níveis de eNOS, suprimiu a infiltração de macrófagos no tecido renal e inibiu a ativação do NF- B. A EPO protege a função renal e aumenta a sobrevida neste modelo de sepse. A proteção da EPO na sepse é dependente, em parte, da inibição do NF- B e do aumento da expressão de eNOS / The pathophysiology of sepsis involves complex cytokine and inflammatory mediator networks, a mechanism to which nuclear factor-kappa B (NF- B ) activation is central. Downregulation of endothelial nitric oxide synthase (eNOS) contributes to sepsis-induced endothelial dysfunction. Erythropoietin (EPO) has emerged as a major tissue-protective cytokine in the setting of stress. We investigated the role of EPO in sepsis-related acute kidney injury (AKI) using a cecal ligation and puncture (CLP) model. Wistar rats were divided into three groups: control (sham-operated); CLP-only; and CLP+EPO. The EPO (4000 IU/kg BW, i.p.) was administered 24 h and 1 h before CLP. To study the early and late effects of EPO on sepsis-induced AKI, we performed experiments at 24 h and 48 h after CLP/sham operation, and we plotted the survival curves. At post-procedure hour 24, CLP+EPO rats presented significantly higher inulin clearance than did CLP-only rats; EPO treatment restored hematocrit levels, as well as mean arterial pressure and metabolic balance. At post-procedure hour 48, CLP+EPO rats presented significantly higher creatinine clearance than did CLP-only rats; EPO treatment restored eNOS levels, suppressed macrophage infiltration, and inhibited NF-B activation,thereby increasing survival. In conclusion, EPO protects renal function and increases survival in this model of sepsis-induced AKI. This protection is dependent on eNOS activation and is partly due to inhibition of the inflammatory response via downregulation of NF- B

A sepse envolve mecanismos complexos de respostas imunológicas e inflamatórias, e o papel do NF- B é essencial. A diminuição da NO sintase endotelial (eNOS) durante a sepse contribui com a disfunção endotelial. A eritropoietina (EPO) é uma citocina protetora de diversos tecidos durante o estresse. Investigamos o papel da EPO na injúria renal aguda (IRA) induzida pela sepse usando o modelo de ligadura e punção do ceco (LPC). Ratos Wistar foram divididos em três grupos: controle; LPC e LPC+EPO (EPO, 4.000UI/kg, administrada 24h e 1h antes da cirurgia). Com a finalidade de estudar os efeitos precoces e tardios da EPO sobre a IRA induzida pela sepse realizamos três etapas de experimentos: Primeira etapa: 24 horas após LPC; Segunda etapa: 48 horas após LPC; Terceira etapa: análise de sobrevida. No estudo precoce o grupo LPC+EPO apresentou clearance de inulina significativamente maior que o grupo LPC. Recuperou os níveis de hematócrito na sepse, melhorou a pressão arterial e a acidose metabólica. No estudo tardio o grupo LPC+EPO apresentou clearance de creatinina significativamente maior que o grupo LPC. Nesta fase tardia a EPO recuperou os níveis de eNOS, suprimiu a infiltração de macrófagos no tecido renal e inibiu a ativação do NF- B. A EPO protege a função renal e aumenta a sobrevida neste modelo de sepse. A proteção da EPO na sepse é dependente, em parte, da inibição do NF- B e do aumento da expressão de eNOS / The pathophysiology of sepsis involves complex cytokine and inflammatory mediator networks, a mechanism to which nuclear factor-kappa B (NF- B ) activation is central. Downregulation of endothelial nitric oxide synthase (eNOS) contributes to sepsis-induced endothelial dysfunction. Erythropoietin (EPO) has emerged as a major tissue-protective cytokine in the setting of stress. We investigated the role of EPO in sepsis-related acute kidney injury (AKI) using a cecal ligation and puncture (CLP) model. Wistar rats were divided into three groups: control (sham-operated); CLP-only; and CLP+EPO. The EPO (4000 IU/kg BW, i.p.) was administered 24 h and 1 h before CLP. To study the early and late effects of EPO on sepsis-induced AKI, we performed experiments at 24 h and 48 h after CLP/sham operation, and we plotted the survival curves. At post-procedure hour 24, CLP+EPO rats presented significantly higher inulin clearance than did CLP-only rats; EPO treatment restored hematocrit levels, as well as mean arterial pressure and metabolic balance. At post-procedure hour 48, CLP+EPO rats presented significantly higher creatinine clearance than did CLP-only rats; EPO treatment restored eNOS levels, suppressed macrophage infiltration, and inhibited NF-B activation,thereby increasing survival. In conclusion, EPO protects renal function and increases survival in this model of sepsis-induced AKI. This protection is dependent on eNOS activation and is partly due to inhibition of the inflammatory response via downregulation of NF- B

Indiana University-Purdue University Indianapolis (IUPUI)