Les interactions hôte-pathogène sont un jeu vaste et complexe entre agent pathogène et hôtepour la victoire de la bataille de la pathogenèse. Plusieurs organismes modèles sont étudiéspour illustrer les mécanismes impliqués dans ces interactions. Dans ma thèse, j'ai utilisé lesplanaires comme un organisme modèle pour explorer les interactions hôte-pathogène. Comme les différents organismes modèles peuvent mettre enévidence les différentes caractéristiques de l'immunité, j'ai décidé de tirer avantage del'absence de connaissances sur l'immunité des planaires en explorant l'inexplorée. Dans monprojet, j'ai infecté les planaires avec 16 bactéries pathogènes : les planaires y sont très résistantes. Pour en explorer lemécanisme j'ai effectué un profilage du transcriptome à partir deplanaires infectées, suivie par un criblage par ARN interférence des gènes up-régulés. J'aidécouvert les gènes qui régissent la résistance antibactérienne dans les planaires, et de façonintéressante, le criblage a permis de mettre en évidence un gène, MORN2, dont la fonctionimmunologique était complètement inconnue. L'induction et l'extinction de l'expression de MORN2dans les macrophages ont révélé que MORN2 contrôle l'internalisation, la réplication et letrafic des bactéries à l'intérieur de la cellule. Dans mon étude, j'ai démontré que MORN2 estun composant de la phagocytose associée à LC3 et qu'il peut surmonter le blocage de lafusion phagolysosomale imposée par les bactéries pathogènes. Ainsi ma thèse met en avantl'importance d'utiliser des organismes modèles inhabituels afin de dévoiler des mécanismesinexplorées et des molécules impliquées dans les interactions hôte-pathogène. / Host-pathogen interaction is a vast and complex interplay between pathogen and hostto conquer the battle of pathogenesis. Several model organisms are being studied to illustratethe mechanisms involved in these interactions. In my thesis I have used planarians as a modelorganism to explore host-pathogen interactions. As different model organismscan highlight different features of immunity I decided to take advantage of lack of knowledgeabout planarian immunity and get benefits from exploring unexplored. In my project I haveinfected planarians with 16 pathogenic bacteria and I found that in contrary to othercommonly used model organisms such as Drosophila, C. elegans and zebrafish the planariansare highly resistant to bacterial infections. To explore the mechanism behind this resistance Iperformed infection induced transcriptome profiling followed by RNA interference screeningof up-regulated gens. I discovered genes governing antibacterial resistance in planarians andinterestingly the screening highlighted a gene MORN2 of which the immunological functionwas completely unknown. The human ortholog of MORN2 is then further assessed for itsantimicrobial function. Induced expression and down regulation of MORN2 in macrophagesrevealed that MORN2 controls uptake, replication and trafficking of bacteria inside the cell.In my study I demonstrated that MORN2 is a component of LC3-associated phagocytosis andit can overcome phagosome maturation blockage imposed by pathogenic bacteria. Thus mythesis propounds the importance of using unusual model organisms to unveil unexploredmechanisms and molecules involved in host-pathogen interactions.

Tropheryma whipplei a longtemps été uniquement considérée comme l’agent responsable de la maladie de Whipple, une affection rare caractérisée notamment par une perte de poids, des diarrhées chroniques et des douleurs abdominales. Toutefois, au cours de ces dernières années, il est apparu que les infections à T. whipplei peuvent présenter des manifestations cliniques communes telles que des pneumonies, des bactériémies fébriles ou des gastroentérites, ce qui montre que la maladie de Whipple ne constitue pas la seule manifestation de l’infection à T. whipplei. Ma thèse a eu deux objectifs. Le premier a été de caractériser l’interaction entre T. whipplei et la cellule dans laquelle elle se réplique, le macrophage. J’ai montré en utilisant diverses techniques (biologie moléculaire à haut débit, biologie cellulaire et biochimie) que T. whipplei induit une réponse macrophagique inédite caractérisée par une polarisation M2 associée à une réponse interféron de type I. J’ai également montré que ces événements sont associés à l’apoptose des macrophages dont l’induction se fait par voie extrinsèque et que l’IL-16, pour laquelle un rôle au cours de l’infection à T. whipplei était avéré, intervient d’une part dans le blocage de la maturation phagosomale et d’autre part interfère avec l’activation des macrophages. Mon second objectif a été de montrer à travers un modèle animal que la primo-infection par T. whipplei se manifeste par une gastroentérite auto-résolutive. Cet objectif découlait directement de travaux récents qui associent T. whipplei à diverses manifestations cliniques et notamment à des épisodes diarrhéiques chez l’enfant. Mes résultats confortent clairement cette hypothèse et montrent également que des dommages préexistants de la muqueuse intestinale permet l’établissement de l’infection à T. whipplei. / Tropheryma whipplei has only been considered as the agent of Whipple‘s disease, a rare disease characterized by weight loss, chronic diarrheas and abdominal pains. It is now believed that infections with T. whipplei result in common clinical manifestations, such as pneumonia, fever, bacteriema or gastroenteritis and, as a consequence, it is likely that the Whipple’s disease is not the only manifestation of T. whipplei infection. During my PhD, I had 2 objectives. The first was to characterize the interaction between T. whipplei and the cell type in which T. whipplei replicates, namely macrophages. I showed using diverse techniques (high throughput molecular biology, cell biology and biochemistry) that T. whipplei induced an unusual macrophage response, characterized by M2 polarization with type I interferon response. I also showed that these events were associated with apoptosis of macrophages induced by the extrinsic pathway and that IL-16, which was already described during T. whipplei infection, was involved in the blockade of the phagosomal maturation and interfered with macrophage activation. The second objective was to show using a murine model that primary infection with T. whipplei results in self-limiting gastroenteritis. This objective directly arose from recent work that associated T. whipplei with various clinical manifestations and, in particular, with diarrheal episodes in children. My results clearly verified this hypothesis and also revealed that pre-existing mucosal damage allowed the establishment of the infection.

“Neglected Rickettsiaceae” (i.e. those harboured by non-hematophagous eukaryotic hosts) display greater phylogenetic variability and more widespread dispersal than pathogenic ones; yet, the knowledge about their actual host range and host shift mechanism is scarce. The present work reports the characterization following the full-cycle rRNA approach (SSU rRNA sequence, specific in situ hybridization, and ultrastructure) of a novel rickettsial bacterium, herewith proposed as 'Candidatus Megaira polyxenophila' gen. nov., sp. nov. We found it in association with four different free-living ciliates (Diophrys oligothrix, Euplotes octocarinatus, Paramecium caudatum, and Spirostomum sp., all belonging to Alveolata, Ciliophora); furthermore it was recently observed as intracellular occurring in Carteria cerasiformis and Pleodorina japonica (Chlorophyceae, Chlorophyta). Phylogenetic analyses demonstrated the belonging of the candidate new genus to the family Rickettsiaceae (Alphaproteobacteria, Rickettsiales) as a sister group of the genus Rickettsia. In situ observations revealed the ability of the candidate new species to colonize either nuclear or cytoplasmic compartments, depending on the host organism. The presence of the same bacterial species within different, evolutionary distant, hosts indicates that 'Candidatus Megaira polyxenophila' recently underwent several distinct host shifts, thus suggesting the existence of horizontal transmission pathways. We consider these findings as indicative of an unexpected spread of rickettsial infections in aquatic communities, possibly by means of trophic interactions, and hence propose a new interpretation of the origin and phylogenetic diversification of rickettsial bacteria.

Tesis por compendio / [ES] La evolución experimental nos permite comprobar postulados teóricos y realizar observaciones que ayuden a incrementar nuestro conocimiento sobre la evolución. Este trabajo tiene como objetivo estudiar la evolución de los virus utilizando enfoques experimentales. Los virus muestran una alta capacidad de evolución, lo que los convierte en modelos perfectos para abordar cuestiones evolutivas con bastante rapidez. Los procesos subyacentes a la evolución y adaptación de los patógenos se rigen por muchos factores: desde la naturaleza intrínseca del virus hasta componentes ambientales que afectan al hospedador, al patógeno y la interacción entre ambos. En esta tesis utilizamos un patosistema formado por una planta y un potyvirus (virus de (+)ssRNA) para explorar cómo diferentes factores bióticos y abióticos modulan la evolución del virus. Primero, exploramos los efectos biológicos de las mutaciones en una proteína del potyvirus, la cual es un componente esencial del complejo de replicación viral. Revelamos las limitaciones evolutivas que operan sobre esta proteína, y que son consecuencia de un equilibrio evolutiva entre la acumulación dentro del huésped y la gravedad de los síntomas. En segundo lugar, examinamos los efectos de la estructura genética de la población del huésped sobre la evolución del virus: evolucionamos virus en poblaciones genéticamente homogéneas de plantas con diferentes susceptibilidades a la infección y en una población heterogénea. Con este trabajo ilustramos cómo la diversidad genética de huéspedes en un ecosistema afecta la adaptación del virus, ya que los virus se especializaron más rápidamente en poblaciones homogéneas pero fueron más patógenos en poblaciones heterogéneas. Finalmente, estudiamos el impacto del ambiente sobre la interacción virus-planta. Para esta parte, primero revisamos los posibles efectos beneficiosos de la infección por virus en ciertos entornos hostiles para la planta. Posteriormente estudiamos el efecto de la sequía, una condición ambiental con una incidencia cada vez mayor y que se sabe afecta la fisiología del huésped. Por lo tanto, evolucionamos un virus en huéspedes bajo condiciones de sequía o de riego abundante. Los virus adaptados en condiciones de sequía conferían una mayor tolerancia a la sequía a la planta huésped a través de alteraciones específicas en la expresión génica del huésped y la señalización hormonal. En general, esta tesis contribuye al aumento del conocimiento en biología evolutiva de los virus de ARN de plantas. / [CA] L'evolució experimental ens permet comprovar postulats teòrics i realitzar observacions que ajuden a incrementar el nostre coneixement sobre l'evolució. Aquest treball té com a objectiu estudiar l'evolució dels virus utilitzant enfocaments experimentals. Els virus mostren una alta capacitat d'evolució, la qual cosa els converteix en models perfectes per a abordar qüestions evolutives amb bastant rapidesa. Els processos subjacents a l'evolució i adaptació dels patògens es regeixen per molts factors: des de la naturalesa intrínseca del virus fins a components ambientals que afecten l'hoste, al patogen i la interacció entre tots dos. En aquesta tesi utilitzem un patosistema format per una planta i un potyvirus (virus de (+)ssRNA) per a explorar com diferents factors biòtics i abiòtics modulen l'evolució del virus. Primer, explorem els efectes biològics de les mutacions en una proteïna del potyvirus, la qual és un component essencial del complex de replicació viral. Revelem les limitacions evolutives que operen sobre aquesta proteïna, i que són conseqüència d'un equilibri evolutiva entre l'acumulació dins de l'hoste i la gravetat dels símptomes. En segon lloc, examinem els efectes de l'estructura genètica de la població de l'hoste sobre l'evolució del virus: evolucionem virus en poblacions genèticament homogènies de plantes amb diferents susceptibilitats a la infecció i en una població heterogènia. Amb aquest treball il·lustrem com la diversitat genètica d'hostes en un ecosistema afecta l'adaptació del virus, ja que els virus es van especialitzar més ràpidament en poblacions homogènies però van ser més patògens en poblacions heterogènies. Finalment, estudiem l'impacte de l'ambient sobre la interacció virus-planta. Per a aquesta part, primer revisem els possibles efectes beneficiosos de la infecció per virus en uns certs entorns hostils per a la planta. Posteriorment estudiem l'efecte de la sequera, una condició ambiental amb una incidència cada vegada major i que se sap afecta la fisiologia de l'hoste. Per tant, evolucionem un virus en hostes sota condicions de sequera o de reg abundant. Els virus adaptats en condicions de sequera conferien una major tolerància a la sequera a la planta hoste a través d'alteracions específiques en l'expressió gènica de l'hoste i la senyalització hormonal. En general, aquesta tesi contribueix a l'augment del coneixement en biologia evolutiva dels virus d'ARN de plantes. / [EN] Experimental evolution allows us to test theoretical postulates and make observations that help increase our knowledge about Evolution. This work aims to use experimental approaches to study the evolution of viruses. Viruses have a high degree of evolvability, which makes them perfect subjects to address evolutionary questions quite rapidly. The underlying processes of pathogen evolution are governed by many factors. These factors can be affecting the virus adaptation at different levels: from the intrinsic virus nature to environmental factors affecting the host, the pathogen and the interaction between both. In this thesis, we used a pathosystem formed by a plant and a potyvirus (+ssRNA virus). Using this pathosystem we have explored how different factors modulate the virus evolution. First, we explored the biological effects of mutations in a potyvirus protein that is an essential component of the virus replication complex. We unveiled the evolutionary constraints on this viral protein, with an evolutionary tradeoff between within-host accumulation and severity of symptoms. Second, we examined the effects of the host population genetic structure on virus evolution: we evolved viruses in homogeneous populations of plants with different viral susceptibilities and in a heterogeneous population. With this work we illustrated how the genetic diversity of hosts in an ecosystem affects virus adaptation, as viruses specialized faster in homogeneous populations but were more pathogenic in heterogeneous ones. Finally, we studied the impact of the environment. For this part we first reviewed the possible beneficial effects of virus infection under certain environments. Afterwards we studied the effect of drought, an environmental condition with a predicted increased incidence and known to affect the host physiology. Therefore, we evolved a virus in host under either well-watered or drought conditions. The viruses adapted under drought conditions conferred an increased drought tolerance to the host plant through specific alterations in host gene expression and hormonal signaling. Overall, this thesis contributed to the increase in knowledge in evolutionary biology of plant RNA viruses. / González Miguélez, R. (2021). Virus Adaptation at Different Levels: Study on the Evolutionary Effects of Mutations, Host Population Genetic Structure and Environmental Factors in Potyviruses [Tesis doctoral]. Universitat Politècnica de València. https://doi.org/10.4995/Thesis/10251/178154 / TESIS / Compendio

Bisher gibt es keine effektive Impfung gegen Malaria und der beste immunologische Schutz wird durch wiederholte intravenöse Injektion von nicht-vermehrungsfähigen Sporozoiten erreicht. Im Gegensatz dazu bietet die Infektion im Blutstadium nur eine Teilimmunität gegen schwere Verläufe der Krankheit. Um beide Prozesse besser zu verstehen, ist eine tiefgehende Untersuchung der Reaktion des angeborenen Immunsystems auf Sporozoiten, sowie Parasiten im Blutstadium erforderlich. Erkenntnisse hieraus können dabei helfen, die Überlegenheit des Sporozoiten-Impfstoffs zu verstehen und, letztendlich, seine Wirksamkeit in einem sichereren, kostengünstigeren und skalierbaren Impfstoff zu rekapitulieren. Um sterile Sporozoiten aus Mückenprärationen für in-vitro experimente zu gewinnen, wurden die Parasiten FACS sortiert und anschließend mit Makrophagen co-kultivert. RNA Sequenzierung der Makrophagen, zeigte ein von Sporozoiten induziertes Expressionsprofil, das durch die Expression von inflammatorischen Genen gekennzeichnet ist. Insbesondere CD201 wurde auf Makrophagen stark hochreguliert und könnte eine Rolle bei der gamma-delta T-Zell-Aktivierung spielen. Darüber hinaus kann gezeigt werden, dass die Aktivierung von Makrophagen durch Sporozoiten teilweise von TLR2 und MyD88 abhängig ist. Interessanterweise waren die genetischen Signaturen „Reaktion auf Verwundung" und „Makroautophagie" in Makrophagen überrepräsentiert die mit Sporozoiten co-kultiviert wurden und sind wahrscheinlich Folgen von aktiver Sporozoiten-Traversierung durch Makrophagen. In der Tat zeigten Mäuse, die mit Traversierungs-defizienten Sporozoiten geimpft wurden stark reduzierte CD8 T-Zell Antworten. Dies deutet auf eine mögliche Rolle der Zelltraversion bei der Induktion effektiver adaptiver Immunantworten hin. Insgesamt tragen diese Ergebnisse zu dem Verständnis der angeborenen Immunantwort auf Plasmodium-Parasiten bei und bieten weitere Möglichkeiten zur zukünftigen Forschung. / Effective vaccination against malaria remains a critical element in the effort to eradicate the disease. So far, best protection is induced by repeated intravenous injection of irradiated, non-replicating sporozoites. In contrast, blood stage infection only affords semi-immunity after several disease episodes are endured. Therefore, in-depth analyses of innate immune responses to sporozoite and blood stage parasites are needed to understand the superiority of the attenuated sporozoite vaccine and ultimately, to recapitulate its efficacy in a safer, cheaper and more practical vaccine. To probe sporozoite-induced innate cell activation, parasites were flow sorted from salivary gland extracts. In a reductionist system, sorted P. berghei sporozoites were co-cultured with primary mouse macrophages. Transcriptomic analysis of sporozoite-experienced macrophages revealed a distinct expression profile characterized by NF-κB driven expression of inflammatory mediators. In particular, CD201, a CD1d-like transmembrane receptor with lipid presentation capabilities, was strongly upregulated on macrophages and might play a role in gamma-delta T-cell activation. In addition, first evidence is provided that macrophage activation by sporozoites is partly dependent on TLR2 and MyD88. Intriguingly, ‘response to wounding’ and ‘macroautophagy’ signatures were enriched in sporozoite-stimulated macrophages and are likely consequences of active sporozoite traversal through innate cells. Indeed, in vivo vaccination with spect1 knockout sporozoites, which are deficient in cell traversal, induced a defective CD8 T-cell response, showcasing a potential role for cell traversal in the induction of effective adaptive responses. Taken together, these findings open up several interesting avenues for future research which will paint a clearer picture of innate immune responses to Plasmodium parasites.

Streptococcus suis (S. suis) is an important opportunistic pathogen, which can cause septicemia and meningitis in pigs and humans. Previous in vivo observations in S. suisinfected pigs revealed lesions at the choroid plexus (CP). In vitro experiments with primary porcine CP epithelial cells (PCPEC) and human CP epithelial papilloma (HIBCPP) cells demonstrated that S. suis can invade and traverse the CP epithelium, and that the CP contributes to the inflammatory response via cytokine expression. Here, next generation sequencing (RNA-seq) was used to compare global transcriptome profiles of PCPEC and HIBCPP cells challenged with S. suis serotype (ST) 2 infected in vitro, and of pigs infected in vivo. Identified differentially expressed genes (DEGs) were, amongst others, involved in inflammatory responses and hypoxia. The RNA-seq data were validated via quantitative PCR of selected DEGs. Employing Gene Set Enrichment Analysis (GSEA), 18, 28, and 21 enriched hallmark gene sets (GSs) were identified for infected HIBCPP cells, PCPEC, and in the CP of pigs suffering from S. suis ST2 meningitis, respectively, of which eight GSs overlapped between the three different sample sets. The majority of these GSs are involved in cellular signaling and pathways, immune response, and development, including inflammatory response and hypoxia. In contrast, suppressed GSs observed during in vitro and in vivo S. suis ST2 infections included those, which were involved in cellular proliferation and metabolic processes. This study suggests that similar cellular processes occur in infected human and porcine CP epithelial cells, especially in terms of inflammatory response.

<p>  </p> <p>Epstein-Barr virus (EBV) is a complex oncogenic symbiont. The molecular mechanisms governing EBV carcinogenesis remain elusive and the functional interactions between virus and host cells are incompletely defined. Some of the known mechanisms include viral integration into the host genome, expression and mutation(s) of viral genes and the host response to the virus. Despite decades of research there is a lack of effective treatment options for EBV-positive cancer patients underscoring an urgent need to further investigate the mechanisms underlying tumorigenesis as well as explore and develop personalized treatment strategies for patients with EBV-positive cancers. In Chapter 1, I introduce Epstein-Barr Virus (EBV), the two phases of EBV lifecycle and an overview of certain EBV-associated carcinomas. I will also discuss the underlying mechanisms and few current therapeutic strategies against EBV infection. Next, I will discuss some of the preclinical model systems and high-throughput computation techniques that are commonly used by researchers in the field of EBV.  </p> <p>In chapter 2, we have systematically analyzed RNA-sequencing from >1000 patients with 15 different cancer types, comparing virus and host factors of EBV+ to EBV- tissues to reveal novel insights into EBV-positive tumors. First, we observed that EBV preferentially integrates at highly accessible regions of the cancer genome with significant enrichment in super-enhancer architecture. Second, we determined that the expression of twelve EBV transcripts, including LMP1 and LMP2, correlated inversely with EBV reactivation signature. Over-expression of these genes significantly suppressed viral reactivation, consistent with a ‘Virostatic’ function. Third, we identified hundreds of novel frequent missense and nonsense variations in Virostatic genes in cancer samples, and that the variant genes failed to regulate their viral and cellular targets in cancer. Lastly, we were able to dichotomously classify EBV-positive tumors based on patterns of host interferon signature genes and immune checkpoint markers, such as PD-L1 and IDO1. </p> <p>In chapter 3, we probed the lifecycle of EBV on a cell-by-cell basis using single cell RNA sequencing (scRNA-seq) data from six EBV-immortalized lymphoblastoid cell lines (LCL). While the majority of LCLs comprised cells containing EBV in the latent phase of its life cycle, we identified two additional clusters that had distinct expression of both host and viral genes. Both clusters were high expressors of EBV Latent Membrane Protein-1 (LMP1) but differed in their expression of other EBV lytic genes, including glycoprotein gene GP350. We further probed into the transcriptional landscape of these clusters to identify potential regulators which will be discussed in further detail in the chapter. Importantly, I was able to demonstrate enhancing HIF1-a signaling by using Pevonedistat, a compound that stabilized HIF1-a can preferentially induce the transcriptional program specific to one of the three identified clusters. </p> <p>In Chapter 4, I describe some of my recent work. In this project, we have used an intuitive <em>in-silico </em>drug prediction approach to rapidly screen and identify FDA-approved or clinically available compounds that can be repurposed to induce lytic cycle in different EBV+ tumors. Using this strategy, we identified Ciclopirox, an antifungal drug, as a potent inducer of lytic cycle in EBV+ epithelial cancers. We used EBV+ GC cells to determine the effect of Ciclopirox on EBV reactivation as well as identify the underlying mechanisms. In summary, we discovered that reactivation of EBV lytic cycle by Ciclopirox is mediated by multiple pathways, two of the major ones being the HIF1-a and NF-kB pathways. Although, Ciclopirox treatment enhanced the killing effect of antiviral, further investigation is needed to effectively deliver this drug <em>in vivo.</em> Throughout this chapter, I have discussed findings that needs further investigation and proposed necessary experiments. Finally, in Chapter 5 I have summarized my work and described how our work can provide novel insights that can help delineate some of the complexities of host-pathogen interactions in EBV-associated malignancies. </p>

Thesis (PhD)--Stellenbosch University, 2013. / ENGLISH ABSTRACT: Mycobacterium tuberculosis, the causative agent of tuberculosis disease, contains five copies of the ESAT-6 gene cluster, each encoding a dedicated ESX protein secretion system which has been defined as a novel Type-VII secretion system. The ESX have been implicated in virulence and survival of M. tuberculosis, and as such present a promising target for novel treatment interventions. This study has investigated the evolution, regulation, functions and substrates of the ESX secretion systems. The evolutionary history of the ESX secretion systems was established using in silico and phylogenetic analyses of the sequenced mycobacteria, closely related actinomycetes and WXG-FtsK clusters from other bacteria. The ESX-4 gene cluster appears to have evolved with the start of the evolution of the mycomembrane, followed by the duplication of ESX-3, which marks the evolution of the genus Mycobacterium. The ESX-1 duplication occurred next, followed by ESX-2 and ESX-5 which occur only in the slow growing mycobacteria. Five additional ESX gene clusters were newly identified and named ESX-P1 to - P5. These additional ESX clusters occur, or are predicted to occur, on plasmid DNA, and appear to be progenitors of the genomic ESX-1 to -5 gene clusters, possibly indicating a plasmid-mediated mechanism of ESX duplication and evolution. The promoters expressing the M. tuberculosis ESX-1 to ESX-5 secretion systems were investigated using a promoter probe assay, and characterised using in silico analyses. Promoters were identified for ESX-1, -2, -3 and -5. The functions of the mycobacterial ESX secretion systems were investigated using whole proteomic, secretomic and metabolomic analyses of the fast growing, non-pathogenic M. smegmatis, which contains three of the ESX secretion systems, ESX-1, 3, and 4. ESX knockout strains of M. smegmatis were generated and used in comparative analyses with wild-type M. smegmatis. ESX-1 was highly expressed in wild-type M. smegmatis, however no specific pathways showed considerable variation when ESX-1 was deleted. Deletion of ESX-3 resulted in substantial variation to multiple cellular pathways, including amino acid, carbohydrate and fatty acid metabolism and oxidative stress. These and other differences indicate possible perturbed polyamine metabolism in the absence of ESX-3. Although no ESX-4 protein components were detected in wild type M. smegmatis, the ESX-4 knockout displayed substantial proteomic variation. Reduced levels of ESX-3 component proteins in the ESX-4 knockout suggest that ESX-4 influences ESX-3 expression. Other variation linked ESX-4 to cell division and molybdenum metabolism. Secretomic analyses of wild-type and ESX knockout M. smegmatis strains were used to search for novel substrates of the M. smegmatis ESX secretion systems. No prototype ESX substrates were identified in the culture filtrates, however 10 possible substrates of the ESX-1, -3 and -4 secretion systems, containing the general ESX secretion signal, YxxxD/E, were identified. The functions of some of these proteins correlate with the ESX functions identified in the proteomic and metabolomic analyses. This study sets the groundwork for future work in understanding the functional roles and expression patterns of these ESX secretion systems and in using global proteomic and metabolomic analyses to understand cellular changes in response to specific signals or genomic changes. / AFRIKAANSE OPSOMMING: Mycobacterium tuberculosis, die veroorsakende agent van tuberkulose, bevat vyf kopieë van die ESAT-6 geengroep, wat elk 'n toegewyde ESX proteïen sekresiesisteem, omskryf as 'n nuwe Tipe-VII sekresiestelsel, kodeer. Die ESX sekresiesisteme is betrokke by virulensie en oorlewing van M. tuberculosis, en is dus belowende teikens vir nuwe behandelings. Hierdie studie het die evolusie, regulasie, funksies en substrate van die ESX sekresiesisteme ondersoek. Die evolusionêre geskiedenis van die ESX sekresiesisteme is bepaal met behulp van in silico en filogenetiese analises van die volgordebepaalde mikobakterieë, nouverwante actinomisete en WXG-FtsK groepe van ander bakterieë. Die ESX-4 geengroep het saam met die evolusie van die mikomembraan ontwikkel, gevolg deur die duplisering van ESX-3, wat die evolusie van die genus Mycobacterium merk. Die ESX-1 duplisering het volgende plaasgevind, gevolg deur ESX-2 en ESX-5, wat slegs in die stadiggroeiende mikobakterieë voorkom. Vyf addisionele ESX geengroepe is nuut geïdentifiseer in hierdie studie en is ESX-P1 tot -P5 genoem. Hierdie addisionale ESX groepe is op, of word voorspel om op, plasmied DNS voor te kom, en mag voorlopers van die genomiese ESX-1 tot -5 geengroepe wees, wat moontlik dui op 'n plasmied-gemedieërde meganisme van ESX duplisering en evolusie. Die promoters wat verantwoordelik is vir die uitdrukking van die M. tuberculosis ESX-1 tot ESX-5 sekresiesisteme is ondersoek deur middel van 'n promoter aktiwiteitstoets, en gekarakteriseer deur in silico analises. Promoters is geidentifiseer vir ESX-1, -2, -3 en -5. Die funksies van die mikobakteriële ESX sekresiesisteme is ondersoek deur proteomiese, sekretomiese en metabolomiese analises van die vinnig-groeiende, nie-patogeniese mikobakterium M. smegmatis, wat ESX- 1, -3 en -4 sekresiesisteme besit. ESX uitslaanmutante van M. smegmatis is gegenereer en gebruik in die vergelykende analises met die wilde-tipe M. smegmatis. ESX-1 is hoogs uitgedruk in wilde-tipe M. smegmatis, maar geen spesifieke metabolise weë het aansienlike variasie getoon wanneer ESX-1 verwyder is. Delesie van ESX-3 het gelei tot aansienlike variasie in verskeie sellulêre weë, insluitend aminosuur-, koolhidraat- en vetsuur-metabolisme en oksidatiewe stres. Hierdie en ander verskille dui op moontlike versteurde poli-amien metabolisme in die afwesigheid van ESX-3. Hoewel geen ESX-4 proteïenkomponente opgespoor is in wilde-tipe M. smegmatis nie, vertoon die ESX-4 uitslaanmutant aansienlike proteomiese variasie. Laer vlakke van ESX-3 proteïne dui daarop dat ESX-4 die uitdrukking van ESX-3 beinvloed. Baie van die proteomiese variasie kan geassosieer word met verlaagde ESX-3 uitdrukking, maar ander variasie mag ESX-4 koppel met seldeling en molibdeen metabolisme. Sekretomiese analises van wilde-tipe en ESX uitslaanmutant M. smegmatis stamme is gebruik om nuwe substrate van die M. smegmatis ESX sekresiesisteme te identifiseer. Geen prototipe ESX substrate is geïdentifiseer in die kultuurfiltraat, maar 10 moontlike substrate van die ESX-1, -3 en -4 sekresiesisteme, met die algemene ESX sekresiesein, YxxxD/E, is geïdentifiseer. Die funksies van sommige van hierdie proteïene korreleer met die funksies geïdentifiseer in die proteomiese en metabolomiese analises. Hierdie studie stel die grondslag vir toekomstige werk in die begrip van die funksionele rol en uitdrukkingspatrone van die ESX sekresiesisteme en in die gebruik van globale proteomiese en metabolomiese analises om sellulêre veranderinge in reaksie op spesifieke seine of genomiese veranderinge te verstaan. / The National Research Foundation / German Academic Exchange Service (DAAD), / The Harry Crossley Foundation / The Ernst and Ethel Erikson Trust / Stellenbosch University

Les levures Candida sont des pathogènes opportunistes responsables d’infections graves chez les patients immunodéprimés. Au cours de ce travail, nous avons développé un modèle cellulaire in vitro pour la caractérisation multiparamétrique des phénotypes d’interaction entre les levures Candida et les macrophages et les neutrophiles, principaux effecteurs de la défense anti-Candida. Il repose sur l’utilisation de marqueurs fluorescents pour le suivi quantitatif de l’interaction en cytométrie en flux et en fluorimétrie. Ce modèle a été validé par la comparaison de l’interaction de trois espèces de levures, C. albicans, C. glabrata et C. lusitaniae, avec des macrophages murins et des neutrophiles humains. Deux stratégies principales de survie des levures à la phagocytose ont été mises en évidence : par la résistance à la phagolyse et la multiplication des levures à l’intérieur des phagocytes jusqu’à leur éclatement, ou par l’évitement de la phagocytose et la multiplication des levures à l’extérieur des phagocytes. L’interprétation des données quantitatives a été confirmée par microscopie à fluorescence et vidéo-microscopie. Afin de mieux comprendre les interactions Candida-phagocytes, nous avons mis au point des outils pour l’analyse fonctionnelle de gènes chez C. lusitaniae. Une stratégie de PCR chevauchante a été développée pour l’obtention de mutants nuls de C. lusitaniae, sans étape de clonage. C’est ainsi que le gène OLE2, codant une Δ9 désaturase d’acides gras potentiellement impliquée dans la biosynthèse de la prostaglandine PGE2, a été invalidé. Le mutant ole2Δ présentait de très nets défauts de filamentation et de reproduction sexuée. Par rapport à une souche sauvage, le mutant ole2∆ était massivement phagocyté par les macrophages, et la survie des phagocytes était plus importante, ce qui suggère un rôle important des lipides insaturés et des oxylipides dans la signalisation cellulaire au cours de l’interaction Candida-phagocytes. Dans la dernière partie de notre travail, nous avons construit une banque de 10 000 mutants de C. lusitaniae par l’intégration aléatoire d’un marqueur dans le génome. Le criblage de cette banque à travers notre modèle cellulaire d’interaction permettra d’identifier de nouveaux gènes impliqués dans l’interaction avec les phagocytes afin de mieux comprendre la physiopathologie des candidoses et de trouver de nouvelles pistes thérapeutiques. / Candida species are opportunistic pathogens causing severe infectious diseases in immunocompromised patients. In this work, we developed a tool for a multi-parameter characterization of the cell interactions between the yeasts Candida and both macrophages and neutrophils, which constitute the main defense against candidiasis. It relies on the labelling of each population with specific fluorescent markers, and on the use of fluorimetry and flow cytometry to assess interactions. The tool has been validated by comparing the interactions of three yeast species C. albicans, C. glabrata and C. lusitaniae, with murine macrophages and human neutrophils. We found that yeasts use two main ways for escaping phagocytosis, which has been confirmed using video-microscopy: either (1) by surviving to phagolysis and dividing into the phagosome until phagocytes burst, or (2) by avoiding phagocytosis and dividing outside phagocytes. In order to better understand the cellular and molecular mechanisms involved in Candida-phagocytes interactions, we developed new molecular tools for the functional analysis of genes in C. lusitaniae, notably a two-step cloning-free PCR-based method for the deletion of genes. This method was successfully used for the deletion of OLE2, a gene encoding a Δ9-desaturase of fatty acids, possibly implicated in prostaglandin PGE2 biosynthesis. The ole2Δ mutant exhibited strong defects in both pseudofilamention and sexual mating. During macrophages infection, ole2Δ yeast cells were massively internalized and triggered less phagocytes cell death than the wild type strain, suggesting that unsaturated fatty acids and/or oxylipids could play a role during interaction with phagocytes. Lastly, a bank of 10,000 mutants was constructed in C. lusitaniae by the random integration of a genetic marker in the genome. The screening of this bank through our tool to analyse cellular interactions will be undertaken to gain insights into understanding of the early stages of the infectious process.

Les biomolécules exercent leurs fonctions en interagissant avec d'autres molécules. Le recensement de l'ensemble des biomolécules et leurs interactions permet de construire leurs réseaux d'interactions et de les analyser sur le plan structural et fonctionnel par des outils bioinformatiques (BiNGO, DAVID). Cela permet d'identifier les biomolécules clés, de prédire de nouvelles fonctions des protéines et de comprendre et modéliser les mécanismes moléculaires d'un processus biologique ou pathologique donné. Les protéines ou régions intrinsèquement désordonnées, qui possèdent une grande plasticité structurale, sont susceptibles d'interagir avec de nombreux partenaires et d'être importantes dans les réseaux d'interactions. A l'aide du prédicteur IUPred, nous avons dans un premier temps cartographié le désordre intrinsèque des protéines dans le réseau d'interactions de la matrice extracellulaire et dans le réseau extracellulaire des protéoglycanes construits à partir de la base de données MatrixDB développée dans l'équipe. Nous avons montré que les protéines très connectées de ces deux réseaux ne sont pas enrichies en désordre. Les fonctions moléculaires surreprésentées dans le jeu de protéines extracellulaires contenant au moins 50% de désordre intrinsèque sont les interactions avec les facteurs de croissance ou les glycosaminoglycanes. Nous avons étudié un jeu de données d'interactions protéine-héparine comportant 118 valeurs de cinétique et nous avons montré une relation positive entre la vitesse d'association des protéines à l'héparine et le pourcentage de désordre de leurs sites de fixation à l'héparine. Nous avons également étudié les interactions de la matrice extracellulaire avec un pathogène, le parasite Leishmania. Nous avons montré que les protéines sécrétées par les Leishmania ne sont pas enrichies en désordre par rapport au protéome. Nous avons établi une liste de onze protéines parasitaires sécrétées possédant au moins trois motifs d'interaction et susceptibles d'interagir avec l'hôte / Biomolecules perform their functions by interacting with other molecules. The identification of all biomolecules and their interactions is required to build their interaction networks. Their structural and functional analysis with bioinformatics tools (BiNGO, DAVID) allow us to identify the key biomolecules, to predict new protein functions and to understand and model the molecular mechanisms of biological or pathological process. Intrinsically disordered proteins or regions, which are characterized by structural plasticity, may interact with many partners and may play a role in the interaction networks. Using the predictor IUPred we mapped the intrinsic disorder in protein interaction networks of the extracellular matrix and of the proteoglycans constructed from the MatrixDB database developed in the laboratory. We have shown that the highest connected proteins of these two networks are not enriched in disorder. The molecular functions overrepresented in the set of extracellular proteins containing at least 50% of intrinsically disordered residues are interactions with growth factors or glycosaminoglycans. We studied a dataset of heparin-protein interactions including 118 kinetic values and we have shown that the association rate of proteins with heparin is related to the intrinsic disorder of heparin-binding sites. We also studied the interactions of the extracellular matrix with a pathogen, the parasite Leishmania. We have shown that proteins secreted by Leishmania are not enriched in disorder compared to their proteome. We have selected eleven parasite proteins containing at least three interaction motifs, which may interact with the host