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Anaplasma phagocytophilum is an obligate intracellular bacterium that infects neutrophils to cause the emerging tick-transmitted disease, human granulocytic anaplasmosis (HGA). Following entry, the pathogen replicates within a host cell-derived vacuole that fails to mature along the endocytic pathway, does not acidify, and does not fuse with lysosomes. Selective fusogenicity is prototypical of many vacuole-adapted pathogens and has been attributed, at least in part, to pathogen modification of the vacuolar inclusion membrane and/or to selective recruitment or exclusion of host trafficking regulators. As a result, the A. phagocytophilum-occupied vacuolar membrane (AVM) provides a unique interface to study the host-pathogen interactions critical to A. phagocytophilum intracellular survival. Diverse vacuole-adapted pathogens; including Chlamydia, Legionella, and Salmonella; selectively recruit host Rab GTPases to their vacuolar membranes to establish replicative permissive niches within their host cells. Rab GTPases coordinate many aspects of endocytic and exocytic cargo delivery. We determined that the A. phagocytophilum-occupied vacuole (ApV) selectively recruits a subset of fluorescently-tagged Rabs that are predominantly associated with recycling endosomes. Another emerging theme among vacuole-adapted pathogens is the ability to hijack ubiquitin machinery to modulate host cellular processes. Mono- and polyubiquitination differentially dictate the subcellular localization, activity, and fate of protein substrates. Monoubiquitination directs membrane traffic from the plasma membrane to the endosome and has been shown to promote autophagy. We show that monoubiquitinated proteins decorate the AVM during infection of promyelocytic HL-60 cells, endothelial RF/6A cells, and to a lesser extent, embryonic tick ISE6 cells. Importantly, tetracycline treatment concomitantly promotes loss of the recycling endosome-associated GFP-Rabs and ubiquitinated proteins and acquisition of the late endosomal marker, Rab7, and lysosomal marker, LAMP-1, implicating bacterial-derived proteins in the ApV's altered fusogenicity. Therefore, we rationalized that A. phagocytophilum-encoded proteins that associate with the AVM may establish interactions with the host cell that are important for intracellular survival. By focusing on A. phagocytophilum proteins that are induced during host infection, we identified the first two bacterial-encoded proteins -- APH_1387 and APH_0032 -- that modify the AVM. Although functional studies are hindered by the lack of a system to genetically manipulate Anaplasma, the pathobiological roles of APH_1387 and APH_0032 are likely unique, as both proteins exhibit very little or no homology with any previously described protein. APH_1387 and APH_0032 are present at the cytoplasmic face of the AVM, therefore they likely interact with host proteins. We demonstrate that ectopic expression of APH_1387 and APH_0032 inhibits the ApV development in A. phagocytophilum infected cells. The results presented in this dissertation contribute to our understanding of how A. phagocytophilum modifies the vacuolar membrane in which it resides to establish a safe haven and evade lysosomal degradation.

RESUME : Le Quorum Sensing est un système de communication bactérien permettant à une population de coordonner l’expression de gènes cibles en fonction de sa densité ou des propriétés du milieu (diffusion, flux....). Chez les bactéries à Gram négatif, le Quorum Sensing est basé sur la synthèse et la détection de petites molécules signal appelées N-acyl-homosérine lactones (AHLs). Les régulateurs transcriptionnels de type LuxR sont les médiateurs de ce système de régulation. Lorsque la concentration en AHLs augmente, ces molécules se fixent au domaine N-terminal d’un régulateur LuxR et provoquent des changement conformationnels entraînant une modification de l’activité du régulateur. Un tel système de régulation a été mis en évidence chez la bactérie Gram négative Brucella melitensis. Cette bactérie pathogène intracellulaire synthétise une dodécanoyl-homosérine lactone (C12-HSL) et possède deux régulateurs de type LuxR : VjbR et BabR. VjbR est impliqué dans la virulence de B. melitensis et est indispensable à l’expression de deux facteurs de virulence: le système flagellaire et le système de sécrétion de type IV VirB. Les C12-HSL ont quant à elles un effet répresseur sur ces deux structures membranaires. Durant ce travail, la mutation du domaine Nterminal du régulateur VjbR a permis de démontrer la capacité de VjbR à médier l’effet des C12-HSL sur l’opéron virB. Les souches mutées dans le gène vjbR forment des agrégats en cultures liquides. Nous avons montré que ce phénotype est lié à la production d’un exopolysaccharide, suggérant pour la première fois que Brucella pourrait former des structures de type biofilm. Cette étude a également permis de mettre en évidence un rôle majeur de VjbR dans la régulation de structures de surface puisque ce régulateur est impliqué dans le contrôle de l’expression de nombreuses protéines de membrane externe (Omp). L’utilisation de la technique d’immunoprécipitation chromatinienne (ChIP) a permis de montrer que VjbR régule directement deux de ces Omps ainsi que l’opéron virB. La virulence de Brucella est en partie basée sur sa capacité à dévier le trafic intracellulaire de ses cellules hôtes (phagocytes professionnels et nonprofessionnels) et à s’y multiplier. Lors de son cycle infectieux, Brucella est confrontée à de nombreux stress et environnements différents, suggérant la nécessité d’une régulation génétique fine en réponse à des stimuli environnementaux. Le Quorum Sensing, de par son implication dans la virulence de ce pathogène pourrait être impliqué dans de telles régulations. Afin d’aborder de façon globale le rôle de VjbR et de BabR chez B. melitensis, des études transcriptomique et protéomique des mutants ΔvjbR et ΔbabR ont été réalisées. Ces études ont permis de mettre en évidence que le Quorum Sensing chez B. melitensis est un système de régulation global, puisqu’il permet de réguler 10% du génome dans les conditions testées (dont 9% sous le contrôle de VjbR). De nombreuses cibles de ces régulateurs sont impliquées dans la virulence et l’adaptation aux conditions de stress (oxydatif, métabolique...), suggérant un rôle important du Quorum Sensing dans l’accomplissement du cycle infectieux de B. melitensis. SUMMARY : Quorum Sensing is a bacterial communication system wich allows the coordinated gene expression within a population regarding its density and environmental properties (diffusion, flow...). In Gram negative bacteria, Quorum Sensing is based on the synthesis and the detection of small diffusible molecules called N-acyl-homoserine lactones (AHLs). LuxR transcriptional regulators are the mediators of these regulation systems. When AHL concentration increases, these molecules bind to the N-terminal domain of a LuxR-type regulator and leads to conformational changes driving the modification of the regulator activity. A similar regulation system has been discovered in the Gram negative bacteria Brucella melitensis. This intracellular pathogen synthesizes a dodecanoylhomoserine lactone (C12-HSL) and possesses two LuxR-type regulators: VjbR and BabR. VjbR is involved in the virulence of this pathogen and is crucial for the expression of two virulence factors : the flagellar system and the type four secretion system VirB. C12-HSL have a repressor effect on these two membrane structures. During this work, mutation of the N-terminal domain of VjbR allowed us to demonstrate the ability of VjbR to mediate C12-HSL effect on the virB operon. vjbR mutated strains aggregate in liquid cultures. We have demonstrated that this phenotype is linked to the production of an exopolysaccharide, suggesting for the first time that Brucella could form biofilm-type structures. This study also demonstrates that VjbR has a major role in the regulation of surface structures because this regulator controls the expression of many outer membrane proteins (Omp). Using the chromatin immunoprecipitation technique (ChIP), we have shown that two of these Omps, as well as the virB operon, are directly regulated by VjbR. The virulence of Brucella is partly based on its ability to deviate the intracellular traffic of its host cells (professional and nonprofessional phagocytes) and to proliferate within these cells. During its infectious cycle, Brucella faces numerous stresses and environments, suggesting the necessity of a finely tuned genetic regulation depending on environmental stimuli. Quorum Sensing, through its involvement in the virulence of this intracellular pathogen, could be involved in such regulations. In order to investigate the role of VjbR and BabR in B. melitensis, global transcriptomic and proteomic studies of ΔvjbR and ΔbabR mutants were performed. These studies demonstrate that Quorum Sensing is a global regulation system in B. melitensis because it controls the expression of 10% of the genome in the condition tested (9% through VjbR). Numerous targets of these two regulators are involved in virulence and adaptation to environmental stresses (oxydative, metabolic...), suggesting an important role of Quorum sensing in the achievement of the infectious cycle of B. melitensis.

Listeria monocytogenes est une bactérie pathogène intracellulaire facultative responsable d’une pathologie grave, la listériose. Si de très nombreux travaux ont permis de caractériser les mécanismes de virulence de cette bactérie, il existe peu de données sur les mécanismes conduisant au portage asymptomatique de L. monocytogenes dans les hôtes mammifères. L’un de ces mécanismes pourrait être une phase de persistance intracellulaire. Lors d’infections prolongées de cellules épithéliales humaines en culture, comme des hépatocytes et des cellules de trophoblastes, L. monocytogenes change de mode de vie intracellulaire. Après la phase active de dissémination de cellule en cellule, les bactéries arrêtent de polymériser l’actine et se retrouvent piégées dans des vacuoles à simple membrane marquées par la protéine endosomale LAMP1. L’objectif de ma thèse était de caractériser ces « Listeria-Containing Vacuoles » (LisCVs). Nous avons montré que les LisCVs sont des compartiments acides, partiellement-dégradatifs, marquées par la protéase lysosomale cathépsine D. Leur formation coïncide avec la disparition du facteur de polymérisation d’actine ActA de la surface bactérienne et la capture des bactéries cytosoliques dépourvues d’actine par des membranes cellulaires. Dans ces compartiments, les bactéries entrent en croissance ralentie ; une sous-population résiste aux stress et peut survivre au-delà de trois jours d’infection. L’utilisation de la gentamicine lors du protocole d’infection n’est pas responsable de la formation des LisCVs. Cependant, cet antibiotique permet la sélection des bactéries vacuolaires, en inhibant spécifiquement la croissance des bactéries cytosoliques. La formation des LisCVs n’est pas spécifique des souches de laboratoire. Toutefois l’efficacité du phénomène pourrait diverger selon les séquençotypes des souches de L. monocytogenes. Les bactéries vacuolaires ont la capacité de sortir des vacuoles et de retourner vers un état motile et réplicatif, après le passage des cellules infectées. Lorsque l’expression du gène actA reste inactive, comme dans les mutants ∆actA, des formes de Listeria vacuolaires persistent dans les cellules hôtes dans un état viable mais non cultivable (VBNC). Ces formes VBNC peuvent être transmises au cours des divisions des cellules hôtes. L’ensemble de ces résultats révèle une nouvelle phase de persistance dans le processus infectieux intracellulaire de L. monocytogenes lors des infections prolongées de certaines cellules épithéliales. Cette propriété pourrait contribuer au portage asymptomatique de ce pathogène dans les tissus épithéliaux, allonger la période d'incubation de la listériose, et rendre les bactéries tolérantes à l’antibiothérapie. / Listeria monocytogenes is a facultative intracellular pathogenic bacterium responsible for a serious disease, listeriosis. Although much work has been done to characterize the virulence mechanisms of this bacterium, there is little data on the mechanisms leading to the asymptomatic carriage of L. monocytogenes in mammalian hosts. One of these mechanisms could be a phase of intracellular persistence. During prolonged infections of human epithelial cells in culture, such as hepatocytes and trophoblast cells, L. monocytogenes changes its intracellular lifestyle. After the active phase of cell-to-cell spread, the bacteria stop polymerizing actin and become trapped in single-membrane vacuoles labeled with the endosomal protein LAMP1.The aim of my thesis was to characterize these "Listeria-Containing Vacuoles" (LisCVs). We have shown that LisCVs are acidic, partially degradative compartments, labeled by the lysosomal protease cathepsin D. Their formation coincides with the disappearance of actin polymerization factor ActA from the bacterial surface and the capture of actin-free cytosolic bacteria by cell membranes. In these compartments, bacterial growth is slowed; a subpopulation is resistant to stress and can survive beyond three days of infection. The use of gentamicin during the infection protocol is not responsible for the formation of LisCVs. However, this antibiotic allows selection of vacuolar bacteria, by specifically inhibiting the growth of cytosolic bacteria. The formation of LisCVs is not specific to laboratory strains. However, the efficacy of the phenomenon could diverge according to the sequence types of L. monocytogenes strains. Vacuolar bacteria have the ability to exit the vacuoles and return to a motile and replicative state during the subculture of infected cells. When expression of the actA gene remains inactive, as in ΔactA mutants, vacuolar Listeria forms persist in host cells in a viable but non-culturable (VBNC) state. These VBNC forms can be transmitted during host cell divisions. All these results reveal a new phase of persistence in the intracellular infectious process of L. monocytogenes during prolonged infections of a subset of epithelial cells. This property could contribute to asymptomatic carriage of this pathogen in epithelial tissues, extend the incubation period of listeriosis, and make bacteria tolerant to antibiotic therapy.

Fusobacterium nucleatum is a Gram-negative, anaerobic bacterium that is a member of the human oral microbiota. Although it is a normal resident of the mouth, it is associated with a number of human diseases including: sepsis, inflammatory bowel disease (IBD), and colorectal cancer (CRC). Despite the important association of F. nucleatum with human health and disease, remarkably little is known about the molecular mechanisms underlying these infections. This knowledge gap can, in part, be attributed to a lack of molecular tools and experimental workflows. Creating the genetic tools to fill this knowledge gap is an imperative undertaking for the future development of treatments for diseases involving F. nucleatum. Previous work in the field has assigned functions to just a handful of Fusobacterium proteins (Fap2, FadA), and only two of those proteins have a well-defined role in the host-pathogen relationship. This dissertation contains work that lays the molecular and genetic foundation for future studies involving F. nucleatum by creating a unique gene deletion system while simultaneously establishing broadly applicable experimental workflows and molecular tools to study initial bacterial attachment and invasion processes crucial to Fusobacterium virulence. Marker-less gene deletions confirm the importance of Fap2 in host-cell attachment and invasion and suggest a lesser role in invasion for FadA, representing a significant revision to the Fusobacterium-host relationship. Also, our system allows for the overexpression and purification of virulence factors directly from Fusobacterium for the first time. This permits us to study aspects of Fusobacterium protein biology that were previously impossible and will provide further insights into the nature of Fusobacterium virulence. A custom suite of molecular tools was also developed to facilitate recombinant expression of these proteins in general laboratory settings using simple E. coli protein expression systems. We have used these new technologies to express and purify a number of potential Fusobacterium virulence factors as detailed in this dissertation. Also contained in this dissertation is the application of these breakthroughs to probe the function of a novel F. nucleatum outer membrane phospholipase, FplA. Phospholipases are important virulence factors in a number of well-studied human pathogens including Pseudomonas aeruginosa and Legionella pneumophila, where they interfere with host cellular signaling processes to increase intracellular bacterial survival. Our data show that FplA is a Class A1 phospholipase (PLA1) with robust catalytic activity capable of binding to and cleaving a number of lipid types. Additionally, we show that it has the ability to bind to important host signaling lipids including phosphatidylinositol 3, 5-bisphosphate and phosphatidylinositol 3, 4, 5-triphosphate. These data suggest FplA may play a role in manipulating the intracellular processes of host cells. Taken together, work in this dissertation provides tools and experimental frameworks for the future study of F. nucleatum pathogenesis while identifying and initially characterizing a new, potentially significant, virulence factor in FplA. / Doctor of Philosophy