Ce travail traite de la formulation et de la caractérisation de liposomes porteurs de glycolipides synthétiques, en vue du ciblage d'une bactérie : Helicobacter pylori. Après avoir passé en revue les différents systèmes à temps de résidence gastrique prolongé, il décrit la synthèse et l'utilisation de néoglycolipides de type "ancre-espaceur-sucre ", constitué respectivement du cholestérol, du tétraéthylène glycol et enfin du fucose (ou N-acétylglucosamine). Ont été étudiées dans ce travail l'organisation supramoléculaire des néoglycolipides seuls en fonction de leur état d'hydratation, les altérations de la bicouche liposomale suite à l'incorporation du néoglycolipide, l'accessibilité des sucres à la surface des liposomes, la variation du pH intraliposomal en fonction de pH externes acides, et enfin, l'interaction de quatre formulations de liposomes contenant ou non les néoglycolipides avec 2 souches d'H. pylori

La conversion par les thymidylate synthases du désoxyuridine 5'-monophosphate (dUMP) en désoxythymidine 5'-monophosphate (dTMP) est une des étapes clés de la biosynthèse des désoxyribonucléotides pyrimidiques. Chez les procaryotes (bactéries et archées), il existe deux familles de thymidylate synthases non homologues : ThyA et ThyX. La distribution phylogénétique quasi-exclusive des deux familles est complexe et ne suit pas les relations phylogéniques entre les organismes. Les protéines de ces deux familles ne présentent aucune similarité de séquence, de structure et leurs mécanismes et efficacités catalytiques diffèrent. Les travaux présentés dans cette thèse ont permis de montrer que l'activité de ThyX est essentielle à la survie de la bactérie Rhodobacter capsulatus en absence de thymidine exogène. A partir des résultats de tests de complémentation génétique et de la modélisation mathématique du métabolisme des folates nous avons pu mettre en évidence que seulement une faible activité dihydrofolate réductase était nécessaire à la survie des organismes utilisant ThyX. D'autre part, j'ai pu montrer par des approches génétiques et par l'étude statistique de plus de 400 génomes procaryotes que les organismes utilisant ThyX ont une réplication et un taux de croissance lents, et possèdent majoritairement un petit génome. Je propose un modèle dans lequel la faible activité catalytique de ThyX limite la réplication de l'ADN e! t par conséquent l'expansion du génome. Enfin, j'ai étudié le métabolisme des pyrimidines chez la bactérie pathogène humaine, Helicobacter pylori. J'ai pu en particulier mettre en évidence qu'en absence de voie de récupération de l'uracile, cette bactérie est capable de métaboliser un analogue toxique le 5-fluorouracile (5FU), utilisé comme anticancéreux. J'ai par ailleurs montré que l'orotate phosphoribosyltransférase de H. pylori était capable de restaurer l'auxotrophie pour l'uracile d'une souche d'Escherichia coli indiquant que cette enzyme pourrait être responsable de la sensibilité de H. pylori au 5FU. Les travaux présentés dans cette thèse ont permis une meilleure compréhension des conséquences physiologiques de l'utilisation de la thymidylate synthase ThyX. Ils ont notamment permis d'expliquer la distribution apparemment sporadique des deux familles de thymidylate synthases dans le monde procaryote.

Helicobacter pylori est une bactérie qui infecte l'estomac de la moitié de la population mondiale et est impliquée dans la plupart des maladies gastriques, dont les ulcères et le cancer de l'estomac. La bactérie produit deux toxines, CagA et Tipα, qui sont associées avec le développement du cancer. CagA est injectée dans les cellules et interagit avec de nombreuses protéines des voies de signalisation cellulaire. Tipα est secrétée et internalisée dans les cellules gastriques où elle induit la production de cytokines pro-inflammatoires. Dans ce travail de thèse, nous avons tout d'abord étudié les interactions entre un domaine central de CagA et des protéines de H. pylori. Nous avons ensuite identifié de nouveaux fragments solubles de CagA par une méthodologie à ‘'haut-débit''. L'un d'eux, correspondant à l'extrémité C-terminale de la protéine de 33kDa, CagAC33, a été caractérisé par différentes techniques de biochimie et de biophysique. CagAC33 forme des dimères de dimères en solution et des particules en microscopie électronique. De plus, CagAC33 peut être phosphorylé in vitro par les kinases c-Src et c-Abl mais l'efficacité de la phosphorylation dépend de la kinase utilisée. L'étude de l'interaction entre la phosphatase SHP-2 et CagAC33 montre que CagA est dephosphorylée in vitro. Par ailleurs, les structures de deux formes cristallines de Tipα ont été déterminées par cristallographie aux rayons X. La structure du monomère de Tipα adopte un nouveau repliement, et la protéine forme des dimères différents dans les deux formes cristallines. L'étude de la protéine en solution indique qu'un des dimères est sans doute favorisé et suggère que les ponts disulfures identifiés en N-terminal ont un rôle durant la sécrétion de la protéine.

<p>Estimating substitution frequencies at sites that influence (Ka) and do not influence (Ks) the amino acid sequence is important for understanding the dynamics of molecular sequence evolution and the selective pressures that have shaped genetic variation. </p><p>The aim of this work was to gain a deeper understanding of the driving forces of substitution frequency variation in human pathogens. <i>Rickettsia prowazekii</i>, the causative agent of epidemic typhus and <i>Helicobacter pylori</i>, which has been implicated in gastric diseases were used as model systems. A specific focus was on the evolution of orphan genes in <i>Rickettsia</i>. Additionally, adaptive sequence evolution and factors influencing protein evolutionary rates in <i>H. pylori</i> were studied.</p><p>The comparative sequence analyses of orphan genes using Typhus Group (TG) and Spotted Fever Group (SFG) <i>Rickettsia</i>, indicate that orphan genes in the SFG correspond to pseudogenes in the TG and that pseudogenes in the SFG correspond to extensively degraded gene remnants in the TG. The analysis also showed that ancestral gene sequences could be reconstructed from extant gene remnants of closely related species. The studies of split genes in <i>R. conorii</i> indicate that many of the small fragmented ORFs are probably pseudogenes. Analysis of the <i>H. pylori </i>carbamoyl phosphate synthetase provided an opportunity to understand natural selection acting on a protein undergoing adaptive evolution. Factors such as network properties, protein-protein interactions, gene essentiality and chromosomal position on protein evolutionary rates in <i>H. pylori</i> were studied, of which antigenicity and gene location were identified as the strongest factors. </p><p>In conclusion, high Ka/Ks ratios in human pathogens may reflect either adaptive sequence evolution or gene deterioration. Distinguishing between the two is an important task in molecular evolution and also of great relevance for medical microbiology and functional genomics research.</p>

Peu étudiée et méconnue, initialement décrite au début du XXème siècle, Helicobacter pylori fut redécouverte en 1982 par deux chercheurs australiens, JR Warren et BJ Marshall. Ils soutinrent que la plupart des ulcères gastro-duodénaux étaient causés par cette bactérie, et non par le stress ou la nourriture épicée, comme pensé auparavant. Cette découverte révolutionna le monde de la gastroentérologie et leur valut le prix Nobel de physiologie et de médecine 2005. Environ la moitié de la population mondiale est colonisée par H. pylori au niveau de l'estomac. Dans 10 à 20% des cas, l'infection peut évoluer vers un ulcère gastro-duodénal et dans certains cas vers une transformation maligne. Cette infection se soigne classiquement à l'aide d'une trithérapie associant 2 antibiotiques à un inhibiteur de la pompe à protons pour neutraliser l'acidité gastrique. Notre travail de recherche a consisté à analyser la proportion de patients infectés par H. pylori dans une cohorte de plus de 22.000 patients, issus de divers groupes ethniques, vivant en Belgique. Ces souches de H. pylori, isolées dans notre laboratoire, à partir des biopsies gastriques, ont aussi servi à une étude pour suivre l'évolution de la résistance aux antibiotiques ces 20 dernières années afin de proposer des améliorations de la prise en charge thérapeutique de l'infection à H. pylori en Belgique.

Helicobacter pylori infects and persistently colonizes the stomach, which results in gastritis and in some individuals peptic ulcer disease or gastric cancer. Adherence of H. pylori to the epithelium is an important factor for development of disease. Attachment is mediated by the adhesins BabA and SabA that binds the ABO/Leb blood group antigens and sialylated glycoconjugates respectively.  High-affinity attachment could be anticipated to be of disadvantage for H. pylori because epithelial cells have a fast turnover rate and the dislocated and shed epithelial cells would carry attached bacteria to the acidic gastric juice in the lumen. However, here we describe that H. pylori manage to adapt to this innate clearance mechanism by unique acid regulatory binding properties of its adhesins. We propose that pH regulated binding properties enable bacteria to detachment from host cells for chemotactic guided motility and successful return to the more neutral epithelium for a fresh restart of the infectious cycle. By comparison of BabA from different stomach loci we identified amino acid key position for acid regulated binding activity. Previous studies found lower prevalence of Leb-binding among H. pylori isolates from southern Europe compared to Sweden. Here we tested if the reduced prevalence of Leb-binding could be explained by a novel binding mode; in among Spanish strains, we identified S812 that demonstrates preference for multivalent binding to ABO antigens in glycolipids; we found that 812 BabA had drifted in its preferred binding epitope away from the consensus a1,2fucosylation and towards the blood group A and B derivatives. Such epitope drift might in particular optimize binding to ABO antigens in densely packed lipid rafts. In parallel, we studied the influence of BabA for disease progression by an inventory of gastric biopsies. BabA correlated both with the oncoprotein CagA, the VacAs1 toxin and, in addition, to severe disease progression. We further correlate BabA expression with positive secretor phenotype and stronger adhesion of H. pylori in vitro. For functional adherence studies in vitro, we constructed a recombinant Leb-expressing cell lineage that supports BabA mediated H. pylori attachment.

Estimating substitution frequencies at sites that influence (Ka) and do not influence (Ks) the amino acid sequence is important for understanding the dynamics of molecular sequence evolution and the selective pressures that have shaped genetic variation. The aim of this work was to gain a deeper understanding of the driving forces of substitution frequency variation in human pathogens. Rickettsia prowazekii, the causative agent of epidemic typhus and Helicobacter pylori, which has been implicated in gastric diseases were used as model systems. A specific focus was on the evolution of orphan genes in Rickettsia. Additionally, adaptive sequence evolution and factors influencing protein evolutionary rates in H. pylori were studied. The comparative sequence analyses of orphan genes using Typhus Group (TG) and Spotted Fever Group (SFG) Rickettsia, indicate that orphan genes in the SFG correspond to pseudogenes in the TG and that pseudogenes in the SFG correspond to extensively degraded gene remnants in the TG. The analysis also showed that ancestral gene sequences could be reconstructed from extant gene remnants of closely related species. The studies of split genes in R. conorii indicate that many of the small fragmented ORFs are probably pseudogenes. Analysis of the H. pylori carbamoyl phosphate synthetase provided an opportunity to understand natural selection acting on a protein undergoing adaptive evolution. Factors such as network properties, protein-protein interactions, gene essentiality and chromosomal position on protein evolutionary rates in H. pylori were studied, of which antigenicity and gene location were identified as the strongest factors. In conclusion, high Ka/Ks ratios in human pathogens may reflect either adaptive sequence evolution or gene deterioration. Distinguishing between the two is an important task in molecular evolution and also of great relevance for medical microbiology and functional genomics research.

Being among the most prevalent of persistent infectious agents in humans worldwide, Helicobacter pylori induces chronic inflammation (gastritis), which may progress to peptic ulceration and stomach cancer. The ability to adhere to the gastric mucosa is considered to be both a colonization and virulence property of H. pylori. For adherence, H. pylori expresses surface-located attachment proteins (adhesins) that bind to specific receptors in the gastric mucosa. The best characterized H. pylori adhesin-receptor interaction is that between the blood group antigen binding adhesin (BabA) and the fucosylated blood group antigens, which are glycans highly expressed in the gastric mucosa. Our recent results have changed the view of the blood group antigen-specific binding mode of H. pylori. We have tested clinical isolates of H. pylori from human populations worldwide for their ability to bind to ABO blood group antigens. The results revealed that more than 95% of isolates from Sweden, Germany, Spain, Japan and Alaska that bind fucosylated blood group antigens, bind both the Lewis b antigen (Leb) (of blood group O) and the blood group A-related antigen A-Lewis b, i.e. they exhibit a generalist type of binding mode. In contrast, the majority of strains (62%) from South American Amerindians bound best to Leb, i.e. they exhibit a specialist blood group “O antigen” binding mode. This specialization in binding coincides with the unique predominance of blood group O in the South American Amerindian populations. Furthermore, we also showed that H. pylori could switch from specialist to generalist binding modes by chromosomal integration of foreign babA gene fragments. A mutant strain lacking the babA gene turned out to adhere to inflamed gastric epithelium, despite the fact that it did not bind Leb. We identified the receptor to which the mutant binds to as the sialyl-dimeric-Lewis x antigen (sdiLex) and found its expression to be associated with persistent H. pylori infection and chronic inflammation, both in humans and Rhesus monkeys. The cognate sialic acid binding adhesin (SabA) was identified by our ReTagging technique. Deletion of sabA caused loss of H. pylori binding to sialylated glycans, and screening of single colony isolates revealed a high frequency of spontaneous on⇒off phase variation in sLex binding. Using erythrocytes as a model for sialyl dependent cell adhesion, we could show that SabA is the sought-after H. pylori sialyl-dependent hemagglutinin. Swedish clinical H. pylori isolates were analyzed for sialyl-dependent hemagglutination (sia-HA), and the sia-HA titers were found to be highly correlated to the levels of sLex binding. Clinical isolates were shown to exhibit several distinct binding modes for sialylated glycans, which suggest that SabA exhibit polymorphism in binding. We also found that SabA binds to sialylated glycans on neutrophil surfaces by mechanisms involving “selectin mimicry”, and that SabA plays an important role in nonopsonic activation of neutrophils. In the human stomach, H. pylori is exposed to selective pressures such as immune and inflammatory responses, and this is reflected by changes in mucosal glycosylation patterns. The high mutation and recombination rates of H. pylori in combination with bio selection will continuously generate clones that are adapted to changes in individual gastric mucosa. Such adaptive selection contributes to the remarkable diversity in binding modes and to the extraordinary chronicity of H. pylori infections worldwide.

The innate immune system is important in both acute and chronic infection. In this thesis, I investigated the effect of H. pylori infection on 1) DCs, key orchestrators of the immune system, and 2) autophagy, recently identified as an important component of innate immunity. I determined that H. pylori activates the STAT3 pathway in DCs, increasing DC maturation and inducing production of IL-10, IL-12p40 and TNF-α, without IL-12p70. This cytokine profile may favour an immunoregulatory response, promoting persistent H. pylori infection. In addition I determined that H. pylori’s VacA toxin induced autophagy, ROS production and Parkin aggregation which has been implicated in mediating autophagy in response to mitochondrial damage. Thus H. pylori alters these key effectors of innate immunity which may play a role in promoting its chronic infection and disease.

The innate immune system is important in both acute and chronic infection. In this thesis, I investigated the effect of H. pylori infection on 1) DCs, key orchestrators of the immune system, and 2) autophagy, recently identified as an important component of innate immunity. I determined that H. pylori activates the STAT3 pathway in DCs, increasing DC maturation and inducing production of IL-10, IL-12p40 and TNF-α, without IL-12p70. This cytokine profile may favour an immunoregulatory response, promoting persistent H. pylori infection. In addition I determined that H. pylori’s VacA toxin induced autophagy, ROS production and Parkin aggregation which has been implicated in mediating autophagy in response to mitochondrial damage. Thus H. pylori alters these key effectors of innate immunity which may play a role in promoting its chronic infection and disease.